From 4aab2aae5db7ca9be3028e20496370fad9531ae9 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 5 Apr 2023 13:28:33 +0200 Subject: [PATCH 001/109] cicd: prueba dependencies script #TASK-4163 --- .../main/java/org/opencb/opencga/app/cli/main/OpencgaMain.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaMain.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaMain.java index 4fa055dde8c..296b1be2d75 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaMain.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaMain.java @@ -17,6 +17,7 @@ package org.opencb.opencga.app.cli.main; import org.apache.commons.lang3.ArrayUtils; +import org.opencb.commons.utils.PrintUtils; import org.opencb.opencga.app.cli.CliOptionsParser; import org.opencb.opencga.app.cli.GeneralCliOptions; import org.opencb.opencga.app.cli.main.processors.CommandProcessor; @@ -48,6 +49,7 @@ public static void main(String[] args) { parser.printUsage(); System.exit(0); } + PrintUtils.printSpace(); checkLogLevel(args); checkMode(args); logger.debug(Arrays.toString(args)); From e4b4fe5afa4a52f1ae876ba4d0066440d1c2d081 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 5 Apr 2023 13:30:16 +0200 Subject: [PATCH 002/109] cicd: prueba dependencies script #TASK-4163 --- .github/workflows/task.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/task.yml b/.github/workflows/task.yml index 886fd6e05dd..ccce1089592 100644 --- a/.github/workflows/task.yml +++ b/.github/workflows/task.yml @@ -8,7 +8,7 @@ on: jobs: build: - uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop + uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@TASK-4163 with: maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' From 6f9eafabf9495c0c7d64966ec49e97c178111135 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 5 Apr 2023 15:35:20 +0200 Subject: [PATCH 003/109] cicd: prueba local dependencies script #TASK-4163 --- .github/workflows/scripts/get_same_branch.sh | 52 ++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 .github/workflows/scripts/get_same_branch.sh diff --git a/.github/workflows/scripts/get_same_branch.sh b/.github/workflows/scripts/get_same_branch.sh new file mode 100644 index 00000000000..3b8d138a52d --- /dev/null +++ b/.github/workflows/scripts/get_same_branch.sh @@ -0,0 +1,52 @@ +#!/bin/bash + +BRANCH_NAME=$1 + +if [[ -z $BRANCH_NAME ]]; then + echo "The first parameter is mandatory and must be a valid branch name." + exit 1 +fi + +if [[ $BRANCH_NAME != "TASK-"* ]]; then + echo "No need to check dependencies." + exit 0 +fi + +function install(){ + local REPO=$1 + cd /home/runner/work/ + git clone git@github.com:opencb/"$REPO".git + cd "$REPO" + git checkout "$BRANCH_NAME" + local BRANCHES=$(git branch --list $BRANCH_NAME) + if [[ -n $BRANCHES ]]; then + echo "Branch name $BRANCH_NAME already exists." + mvn clean install -DskipTests + else + echo "$BRANCHES Is empty" + fi +} + +PWD=$(pwd) +echo "The absolute exec path is $PWD" + +if [[ "$PWD" != *"java-common-libs"* ]]; then + ## biodata + if [[ "$PWD" == *"biodata"* ]]; then + echo "It's biodata." + install "java-common-libs" + fi + ## cellbase + if [[ "$PWD" == *"cellbase"* ]]; then + echo "It's cellbase." + install "java-common-libs" + install "biodata" + fi + ## opencga + if [[ "$PWD" == *"opencga"* ]]; then + echo "It's opencga." + install "java-common-libs" + install "biodata" + install "cellbase" + fi +fi \ No newline at end of file From 7fb65ed29037031cffd71a75e079014e13bd499e Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 6 Apr 2023 09:50:36 +0200 Subject: [PATCH 004/109] cicd: prueba home workspace #TASK-4163 --- .github/workflows/scripts/get_same_branch.sh | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/scripts/get_same_branch.sh b/.github/workflows/scripts/get_same_branch.sh index 3b8d138a52d..47d31f03b4b 100644 --- a/.github/workflows/scripts/get_same_branch.sh +++ b/.github/workflows/scripts/get_same_branch.sh @@ -14,9 +14,10 @@ fi function install(){ local REPO=$1 - cd /home/runner/work/ + #cd /home/runner/work/ + cd ~ || exit 2 git clone git@github.com:opencb/"$REPO".git - cd "$REPO" + cd "$REPO" || exit 2 git checkout "$BRANCH_NAME" local BRANCHES=$(git branch --list $BRANCH_NAME) if [[ -n $BRANCHES ]]; then From 6eb4f0d2a3d073f7fe3238e29830a2b7404d7dcc Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 6 Apr 2023 13:17:47 +0200 Subject: [PATCH 005/109] cicd: Trying https clone #TASK-4163 --- .github/workflows/scripts/get_same_branch.sh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/scripts/get_same_branch.sh b/.github/workflows/scripts/get_same_branch.sh index 47d31f03b4b..2193aa1a0f9 100644 --- a/.github/workflows/scripts/get_same_branch.sh +++ b/.github/workflows/scripts/get_same_branch.sh @@ -14,9 +14,9 @@ fi function install(){ local REPO=$1 - #cd /home/runner/work/ - cd ~ || exit 2 - git clone git@github.com:opencb/"$REPO".git + cd /home/runner/work/ + #git clone git@github.com:opencb/"$REPO".git + git clone https://github.com/opencb/"$REPO".git cd "$REPO" || exit 2 git checkout "$BRANCH_NAME" local BRANCHES=$(git branch --list $BRANCH_NAME) From 50f4f94e5cc7e83e7dac556cf63b1b87d5721dd4 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 6 Apr 2023 16:24:05 +0200 Subject: [PATCH 006/109] cicd: Reinstalling maven dependencies #TASK-4163 --- .github/workflows/scripts/get_same_branch.sh | 2 +- .github/workflows/test-analysis.yml | 16 ++++++++++++++++ 2 files changed, 17 insertions(+), 1 deletion(-) diff --git a/.github/workflows/scripts/get_same_branch.sh b/.github/workflows/scripts/get_same_branch.sh index 2193aa1a0f9..570bae1525b 100644 --- a/.github/workflows/scripts/get_same_branch.sh +++ b/.github/workflows/scripts/get_same_branch.sh @@ -18,7 +18,7 @@ function install(){ #git clone git@github.com:opencb/"$REPO".git git clone https://github.com/opencb/"$REPO".git cd "$REPO" || exit 2 - git checkout "$BRANCH_NAME" + git checkout -b "$BRANCH_NAME" local BRANCHES=$(git branch --list $BRANCH_NAME) if [[ -n $BRANCHES ]]; then echo "Branch name $BRANCH_NAME already exists." diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index 52abb53cb56..101ba4e46b7 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -38,6 +38,14 @@ jobs: distribution: 'temurin' java-version: '11' cache: 'maven' + - name: Install dependencies branches + run: | + if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then + chmod +x ./.github/workflows/scripts/get_same_branch.sh + ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }} + else + echo "./.github/workflows/scripts/get_same_branch.sh does not exist." + fi - name: Test and Analyze env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Needed to get PR information, if any @@ -57,6 +65,14 @@ jobs: distribution: 'temurin' java-version: '8' cache: 'maven' + - name: Install dependencies branches + run: | + if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then + chmod +x ./.github/workflows/scripts/get_same_branch.sh + ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }} + else + echo "./.github/workflows/scripts/get_same_branch.sh does not exist." + fi - name: Install Samtools run: sudo apt-get install samtools python3-deeptools - name: Start MongoDB v6.0 From a04c478062a49438bf19cb178c4bb8d1f12a2f4a Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 11 Apr 2023 13:47:53 +0200 Subject: [PATCH 007/109] cicd: save maven cache #TASK-4163 --- .github/workflows/test-analysis.yml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index 101ba4e46b7..b8f9f09d4da 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -46,6 +46,10 @@ jobs: else echo "./.github/workflows/scripts/get_same_branch.sh does not exist." fi + - name: Save Maven cache + uses: skjolber/maven-cache-github-action@v1 + with: + step: save - name: Test and Analyze env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Needed to get PR information, if any @@ -73,6 +77,10 @@ jobs: else echo "./.github/workflows/scripts/get_same_branch.sh does not exist." fi + - name: Save Maven cache + uses: skjolber/maven-cache-github-action@v1 + with: + step: save - name: Install Samtools run: sudo apt-get install samtools python3-deeptools - name: Start MongoDB v6.0 From 46b5e9118018d6212331775d874799f501a37f30 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 11 Apr 2023 14:56:21 +0200 Subject: [PATCH 008/109] cicd: git branch -r --list #TASK-4163 --- .github/workflows/scripts/get_same_branch.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/scripts/get_same_branch.sh b/.github/workflows/scripts/get_same_branch.sh index 570bae1525b..f07755be3b6 100644 --- a/.github/workflows/scripts/get_same_branch.sh +++ b/.github/workflows/scripts/get_same_branch.sh @@ -19,7 +19,8 @@ function install(){ git clone https://github.com/opencb/"$REPO".git cd "$REPO" || exit 2 git checkout -b "$BRANCH_NAME" - local BRANCHES=$(git branch --list $BRANCH_NAME) + local BRANCHES="" + BRANCHES=$(git branch -r --list $BRANCH_NAME) if [[ -n $BRANCHES ]]; then echo "Branch name $BRANCH_NAME already exists." mvn clean install -DskipTests From 7a8885a9e184b4bc8273c34b7fef1bfef2183d83 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 11 Apr 2023 15:00:22 +0200 Subject: [PATCH 009/109] cicd: git branch -r --list #TASK-4163 --- .github/workflows/scripts/get_same_branch.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/scripts/get_same_branch.sh b/.github/workflows/scripts/get_same_branch.sh index f07755be3b6..36a385891a0 100644 --- a/.github/workflows/scripts/get_same_branch.sh +++ b/.github/workflows/scripts/get_same_branch.sh @@ -18,9 +18,9 @@ function install(){ #git clone git@github.com:opencb/"$REPO".git git clone https://github.com/opencb/"$REPO".git cd "$REPO" || exit 2 - git checkout -b "$BRANCH_NAME" + git checkout -b origin/"$BRANCH_NAME" local BRANCHES="" - BRANCHES=$(git branch -r --list $BRANCH_NAME) + BRANCHES=$(git branch -r --list origin/$BRANCH_NAME) if [[ -n $BRANCHES ]]; then echo "Branch name $BRANCH_NAME already exists." mvn clean install -DskipTests From 445064d1da75f471247b01acff2141b94a4cb6ba Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 11 Apr 2023 15:17:52 +0200 Subject: [PATCH 010/109] cicd: current branch name check #TASK-4163 --- .github/workflows/scripts/get_same_branch.sh | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/.github/workflows/scripts/get_same_branch.sh b/.github/workflows/scripts/get_same_branch.sh index 36a385891a0..a06f39cff5f 100644 --- a/.github/workflows/scripts/get_same_branch.sh +++ b/.github/workflows/scripts/get_same_branch.sh @@ -21,6 +21,13 @@ function install(){ git checkout -b origin/"$BRANCH_NAME" local BRANCHES="" BRANCHES=$(git branch -r --list origin/$BRANCH_NAME) + CURRENT=$(git branch --show-current) + echo "Current branch name $CURRENT" + if [[ "$CURRENT" == "$BRANCH_NAME" ]]; then + echo "$CURRENT Branch is equals $BRANCH_NAME " + else + echo "$CURRENT Branch is NOT EQUALS $BRANCH_NAME " + fi if [[ -n $BRANCHES ]]; then echo "Branch name $BRANCH_NAME already exists." mvn clean install -DskipTests From aea63291caedd0af96f0f6e2f35e6bbac7d89d62 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 11 Apr 2023 15:23:02 +0200 Subject: [PATCH 011/109] cicd: git checkout origin/branch_name #TASK-4163 --- .github/workflows/scripts/get_same_branch.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/scripts/get_same_branch.sh b/.github/workflows/scripts/get_same_branch.sh index a06f39cff5f..421af126aa4 100644 --- a/.github/workflows/scripts/get_same_branch.sh +++ b/.github/workflows/scripts/get_same_branch.sh @@ -18,7 +18,7 @@ function install(){ #git clone git@github.com:opencb/"$REPO".git git clone https://github.com/opencb/"$REPO".git cd "$REPO" || exit 2 - git checkout -b origin/"$BRANCH_NAME" + git checkout origin/"$BRANCH_NAME" local BRANCHES="" BRANCHES=$(git branch -r --list origin/$BRANCH_NAME) CURRENT=$(git branch --show-current) From a0a11e7057073fb56b1d2e819f704b74ec5557e8 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 11 Apr 2023 15:25:33 +0200 Subject: [PATCH 012/109] cicd: git checkout branch_name #TASK-4163 --- .github/workflows/scripts/get_same_branch.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/scripts/get_same_branch.sh b/.github/workflows/scripts/get_same_branch.sh index 421af126aa4..19eea1a9fad 100644 --- a/.github/workflows/scripts/get_same_branch.sh +++ b/.github/workflows/scripts/get_same_branch.sh @@ -18,7 +18,7 @@ function install(){ #git clone git@github.com:opencb/"$REPO".git git clone https://github.com/opencb/"$REPO".git cd "$REPO" || exit 2 - git checkout origin/"$BRANCH_NAME" + git checkout "$BRANCH_NAME" local BRANCHES="" BRANCHES=$(git branch -r --list origin/$BRANCH_NAME) CURRENT=$(git branch --show-current) From 154a81a6320b481a049c557d740cc3d419e76b94 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 11 Apr 2023 15:58:53 +0200 Subject: [PATCH 013/109] cicd: checkout and clean unuseful code #TASK-4163 --- .github/workflows/scripts/get_same_branch.sh | 13 ++---- .github/workflows/test-analysis.yml | 48 ++++++++++---------- 2 files changed, 27 insertions(+), 34 deletions(-) diff --git a/.github/workflows/scripts/get_same_branch.sh b/.github/workflows/scripts/get_same_branch.sh index 19eea1a9fad..4c0b140795d 100644 --- a/.github/workflows/scripts/get_same_branch.sh +++ b/.github/workflows/scripts/get_same_branch.sh @@ -14,25 +14,18 @@ fi function install(){ local REPO=$1 - cd /home/runner/work/ + cd /home/runner/work/ || exit 2 #git clone git@github.com:opencb/"$REPO".git git clone https://github.com/opencb/"$REPO".git cd "$REPO" || exit 2 git checkout "$BRANCH_NAME" - local BRANCHES="" - BRANCHES=$(git branch -r --list origin/$BRANCH_NAME) CURRENT=$(git branch --show-current) echo "Current branch name $CURRENT" - if [[ "$CURRENT" == "$BRANCH_NAME" ]]; then - echo "$CURRENT Branch is equals $BRANCH_NAME " - else - echo "$CURRENT Branch is NOT EQUALS $BRANCH_NAME " - fi - if [[ -n $BRANCHES ]]; then + if [[ "$CURRENT" == "$BRANCH_NAME" ]]; then echo "Branch name $BRANCH_NAME already exists." mvn clean install -DskipTests else - echo "$BRANCHES Is empty" + echo "$CURRENT Branch is NOT EQUALS $BRANCH_NAME " fi } diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index b8f9f09d4da..2c79137f816 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -38,18 +38,18 @@ jobs: distribution: 'temurin' java-version: '11' cache: 'maven' - - name: Install dependencies branches - run: | - if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then - chmod +x ./.github/workflows/scripts/get_same_branch.sh - ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }} - else - echo "./.github/workflows/scripts/get_same_branch.sh does not exist." - fi - - name: Save Maven cache - uses: skjolber/maven-cache-github-action@v1 - with: - step: save + # - name: Install dependencies branches + # run: | + # if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then + # chmod +x ./.github/workflows/scripts/get_same_branch.sh + # ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }} + # else + # echo "./.github/workflows/scripts/get_same_branch.sh does not exist." + # fi + # - name: Save Maven cache + # uses: skjolber/maven-cache-github-action@v1 + # with: + # step: save - name: Test and Analyze env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Needed to get PR information, if any @@ -69,18 +69,18 @@ jobs: distribution: 'temurin' java-version: '8' cache: 'maven' - - name: Install dependencies branches - run: | - if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then - chmod +x ./.github/workflows/scripts/get_same_branch.sh - ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }} - else - echo "./.github/workflows/scripts/get_same_branch.sh does not exist." - fi - - name: Save Maven cache - uses: skjolber/maven-cache-github-action@v1 - with: - step: save + # - name: Install dependencies branches + # run: | + # if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then + # chmod +x ./.github/workflows/scripts/get_same_branch.sh + # ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }} + # else + # echo "./.github/workflows/scripts/get_same_branch.sh does not exist." + # fi + # - name: Save Maven cache + # uses: skjolber/maven-cache-github-action@v1 + # with: + # step: save - name: Install Samtools run: sudo apt-get install samtools python3-deeptools - name: Start MongoDB v6.0 From 8337eb8a259aeb25eba0345bbae121e7fb610742 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 11 Apr 2023 16:41:35 +0200 Subject: [PATCH 014/109] cicd: maven cache is not available #TASK-4163 --- .github/workflows/test-analysis.yml | 32 ++++++++++++++--------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index 2c79137f816..0064b082542 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -38,14 +38,14 @@ jobs: distribution: 'temurin' java-version: '11' cache: 'maven' - # - name: Install dependencies branches - # run: | - # if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then - # chmod +x ./.github/workflows/scripts/get_same_branch.sh - # ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }} - # else - # echo "./.github/workflows/scripts/get_same_branch.sh does not exist." - # fi + - name: Install dependencies branches + run: | + if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then + chmod +x ./.github/workflows/scripts/get_same_branch.sh + ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }} + else + echo "./.github/workflows/scripts/get_same_branch.sh does not exist." + fi # - name: Save Maven cache # uses: skjolber/maven-cache-github-action@v1 # with: @@ -69,14 +69,14 @@ jobs: distribution: 'temurin' java-version: '8' cache: 'maven' - # - name: Install dependencies branches - # run: | - # if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then - # chmod +x ./.github/workflows/scripts/get_same_branch.sh - # ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }} - # else - # echo "./.github/workflows/scripts/get_same_branch.sh does not exist." - # fi + - name: Install dependencies branches + run: | + if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then + chmod +x ./.github/workflows/scripts/get_same_branch.sh + ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }} + else + echo "./.github/workflows/scripts/get_same_branch.sh does not exist." + fi # - name: Save Maven cache # uses: skjolber/maven-cache-github-action@v1 # with: From 455c876ca2305ef9890c19828a871d1e07268593 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 12 Apr 2023 18:26:21 +0200 Subject: [PATCH 015/109] cicd: clean script and workflows #TASK-4163 --- .github/workflows/scripts/get_same_branch.sh | 41 +++----------------- .github/workflows/task.yml | 26 ------------- 2 files changed, 6 insertions(+), 61 deletions(-) diff --git a/.github/workflows/scripts/get_same_branch.sh b/.github/workflows/scripts/get_same_branch.sh index 4c0b140795d..1c0caad9ca4 100644 --- a/.github/workflows/scripts/get_same_branch.sh +++ b/.github/workflows/scripts/get_same_branch.sh @@ -15,40 +15,11 @@ fi function install(){ local REPO=$1 cd /home/runner/work/ || exit 2 - #git clone git@github.com:opencb/"$REPO".git - git clone https://github.com/opencb/"$REPO".git - cd "$REPO" || exit 2 - git checkout "$BRANCH_NAME" - CURRENT=$(git branch --show-current) - echo "Current branch name $CURRENT" - if [[ "$CURRENT" == "$BRANCH_NAME" ]]; then - echo "Branch name $BRANCH_NAME already exists." - mvn clean install -DskipTests - else - echo "$CURRENT Branch is NOT EQUALS $BRANCH_NAME " - fi + git clone https://github.com/opencb/"$REPO".git -b "$BRANCH_NAME" + echo "Branch name $BRANCH_NAME already exists." + mvn clean install -DskipTests } -PWD=$(pwd) -echo "The absolute exec path is $PWD" - -if [[ "$PWD" != *"java-common-libs"* ]]; then - ## biodata - if [[ "$PWD" == *"biodata"* ]]; then - echo "It's biodata." - install "java-common-libs" - fi - ## cellbase - if [[ "$PWD" == *"cellbase"* ]]; then - echo "It's cellbase." - install "java-common-libs" - install "biodata" - fi - ## opencga - if [[ "$PWD" == *"opencga"* ]]; then - echo "It's opencga." - install "java-common-libs" - install "biodata" - install "cellbase" - fi -fi \ No newline at end of file +install "java-common-libs" +install "biodata" +install "cellbase" diff --git a/.github/workflows/task.yml b/.github/workflows/task.yml index ccce1089592..bb6d540de71 100644 --- a/.github/workflows/task.yml +++ b/.github/workflows/task.yml @@ -20,13 +20,6 @@ jobs: test_profile: runShortTests report_context: development - deploy-maven: - name: Deploy in maven only for renamed versions - uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop - needs: [ build, test ] - if: contains( needs.build.outputs.version ,'TASK') - secrets: inherit - deploy-docker: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: test @@ -34,22 +27,3 @@ jobs: cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ github.ref_name }} secrets: inherit - # The following jobs are to see that the previous 'if' doesn't fail and that the maven deploy is executed because it is true - snapshot-version: - name: Check SNAPSHOT version - needs: [ build, test ] - if: contains(needs.build.outputs.version ,'SNAPSHOT') - runs-on: ubuntu-22.04 - steps: - - name: test-version-from-check - run: echo "Project version is " ${{ needs.build.outputs.version }} - - task-version: - name: Check TASK version - needs: [ build, test ] - if: contains(needs.build.outputs.version ,'TASK') - runs-on: ubuntu-22.04 - steps: - - name: test-version-from-check - run: echo "Project version is " ${{ needs.build.outputs.version }} - From 2bdced845a44581066a589a9e65b3fa6b79fe29c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 12 Apr 2023 18:30:37 +0200 Subject: [PATCH 016/109] cicd: clean script and workflows #TASK-4163 --- .github/workflows/scripts/get_same_branch.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/scripts/get_same_branch.sh b/.github/workflows/scripts/get_same_branch.sh index 1c0caad9ca4..cd079000663 100644 --- a/.github/workflows/scripts/get_same_branch.sh +++ b/.github/workflows/scripts/get_same_branch.sh @@ -16,6 +16,7 @@ function install(){ local REPO=$1 cd /home/runner/work/ || exit 2 git clone https://github.com/opencb/"$REPO".git -b "$BRANCH_NAME" + cd "$REPO" || exit 2 echo "Branch name $BRANCH_NAME already exists." mvn clean install -DskipTests } From e748246e48d997cb68084358446d7819f8dee7d0 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 12 Apr 2023 18:32:31 +0200 Subject: [PATCH 017/109] cicd: clean script and workflows #TASK-4163 --- .github/workflows/scripts/get_same_branch.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/scripts/get_same_branch.sh b/.github/workflows/scripts/get_same_branch.sh index cd079000663..04e046c7c91 100644 --- a/.github/workflows/scripts/get_same_branch.sh +++ b/.github/workflows/scripts/get_same_branch.sh @@ -16,7 +16,7 @@ function install(){ local REPO=$1 cd /home/runner/work/ || exit 2 git clone https://github.com/opencb/"$REPO".git -b "$BRANCH_NAME" - cd "$REPO" || exit 2 + cd "$REPO" || exit echo "Branch name $BRANCH_NAME already exists." mvn clean install -DskipTests } From 914cd52933174795ec40621eb0024b8114d1909d Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 12 Apr 2023 18:34:22 +0200 Subject: [PATCH 018/109] cicd: clean script and workflows #TASK-4163 --- .github/workflows/scripts/get_same_branch.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/scripts/get_same_branch.sh b/.github/workflows/scripts/get_same_branch.sh index 04e046c7c91..7980142fb64 100644 --- a/.github/workflows/scripts/get_same_branch.sh +++ b/.github/workflows/scripts/get_same_branch.sh @@ -16,7 +16,7 @@ function install(){ local REPO=$1 cd /home/runner/work/ || exit 2 git clone https://github.com/opencb/"$REPO".git -b "$BRANCH_NAME" - cd "$REPO" || exit + cd "$REPO" || exit 0 echo "Branch name $BRANCH_NAME already exists." mvn clean install -DskipTests } From 7703cce0f76e2c1836e3a7652edb6b11eb79f309 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 12 Apr 2023 18:37:40 +0200 Subject: [PATCH 019/109] cicd: change exit for return in get_same_branch.sh #TASK-4163 --- .github/workflows/scripts/get_same_branch.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/scripts/get_same_branch.sh b/.github/workflows/scripts/get_same_branch.sh index 7980142fb64..f2325fff46d 100644 --- a/.github/workflows/scripts/get_same_branch.sh +++ b/.github/workflows/scripts/get_same_branch.sh @@ -16,7 +16,7 @@ function install(){ local REPO=$1 cd /home/runner/work/ || exit 2 git clone https://github.com/opencb/"$REPO".git -b "$BRANCH_NAME" - cd "$REPO" || exit 0 + cd "$REPO" || return echo "Branch name $BRANCH_NAME already exists." mvn clean install -DskipTests } From cf7744f6a77b46cd1a2833f44ae0f10266547e2c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 12 Apr 2023 18:47:15 +0200 Subject: [PATCH 020/109] cicd: change script get_same_branch.sh to check if directory exists #TASK-4163 --- .github/workflows/scripts/get_same_branch.sh | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/.github/workflows/scripts/get_same_branch.sh b/.github/workflows/scripts/get_same_branch.sh index f2325fff46d..fef5346c0e2 100644 --- a/.github/workflows/scripts/get_same_branch.sh +++ b/.github/workflows/scripts/get_same_branch.sh @@ -15,10 +15,14 @@ fi function install(){ local REPO=$1 cd /home/runner/work/ || exit 2 - git clone https://github.com/opencb/"$REPO".git -b "$BRANCH_NAME" - cd "$REPO" || return - echo "Branch name $BRANCH_NAME already exists." - mvn clean install -DskipTests + git clone https://github.com/opencb/"$REPO".git -d "$BRANCH_NAME" + if [ -d "./$REPO" ]; then + cd "$REPO" || exit 2 + echo "Branch name $BRANCH_NAME already exists." + mvn clean install -DskipTests + else + echo "$CURRENT Branch is NOT EQUALS $BRANCH_NAME " + fi } install "java-common-libs" From 3b415b5db515c16edd19d7d9f6c874ae7dda86b5 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 13 Apr 2023 11:14:43 +0200 Subject: [PATCH 021/109] Cicd: clean comments #TASK-4163 --- .github/workflows/test-analysis.yml | 8 -------- 1 file changed, 8 deletions(-) diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index 0064b082542..760a0d19435 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -46,10 +46,6 @@ jobs: else echo "./.github/workflows/scripts/get_same_branch.sh does not exist." fi - # - name: Save Maven cache - # uses: skjolber/maven-cache-github-action@v1 - # with: - # step: save - name: Test and Analyze env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Needed to get PR information, if any @@ -77,10 +73,6 @@ jobs: else echo "./.github/workflows/scripts/get_same_branch.sh does not exist." fi - # - name: Save Maven cache - # uses: skjolber/maven-cache-github-action@v1 - # with: - # step: save - name: Install Samtools run: sudo apt-get install samtools python3-deeptools - name: Start MongoDB v6.0 From fe8f9e2b72b72a1b19f433a41d3d8bff1bfc9fe7 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 13 Apr 2023 11:55:56 +0200 Subject: [PATCH 022/109] cicd: change script get_same_branch.sh to check if directory exists #TASK-4163 --- .github/workflows/scripts/get_same_branch.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/scripts/get_same_branch.sh b/.github/workflows/scripts/get_same_branch.sh index fef5346c0e2..f217d21e70c 100644 --- a/.github/workflows/scripts/get_same_branch.sh +++ b/.github/workflows/scripts/get_same_branch.sh @@ -15,7 +15,7 @@ fi function install(){ local REPO=$1 cd /home/runner/work/ || exit 2 - git clone https://github.com/opencb/"$REPO".git -d "$BRANCH_NAME" + git clone https://github.com/opencb/"$REPO".git -b "$BRANCH_NAME" if [ -d "./$REPO" ]; then cd "$REPO" || exit 2 echo "Branch name $BRANCH_NAME already exists." From 1b1a91222139baff928fd6c0a728778400507baf Mon Sep 17 00:00:00 2001 From: Juanfe Sanahuja <85166064+juanfeSanahuja@users.noreply.github.com> Date: Fri, 21 Apr 2023 16:33:27 +0200 Subject: [PATCH 023/109] Update test-analysis.yml --- .github/workflows/test-analysis.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index 01cbc7d3d3d..e5c870228e9 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -42,7 +42,8 @@ jobs: run: mvn -T 2 clean install -P storage-hadoop,hdp3.1,${{ inputs.test_profile }} -DskipTests -Dcheckstyle.skip org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=opencb_opencga test: name: Execute JUnit and Jacoco tests - runs-on: ubuntu-22.04 + #runs-on: ubuntu-22.04 + runs-on: self-hosted steps: - uses: actions/checkout@v3 with: From 077892c1e14c05d47badf39586491269435c5870 Mon Sep 17 00:00:00 2001 From: Juanfe Sanahuja <85166064+juanfeSanahuja@users.noreply.github.com> Date: Fri, 21 Apr 2023 16:52:44 +0200 Subject: [PATCH 024/109] Update test-analysis.yml --- .github/workflows/test-analysis.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index e5c870228e9..2a96ffc4ffc 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -48,12 +48,12 @@ jobs: - uses: actions/checkout@v3 with: fetch-depth: '0' - - name: Set up JDK 8 - uses: actions/setup-java@v3 - with: - distribution: 'temurin' - java-version: '8' - cache: 'maven' + #- name: Set up JDK 8 + # uses: actions/setup-java@v3 + # with: + # distribution: 'temurin' + # java-version: '8' + # cache: 'maven' - name: Install Samtools run: sudo apt-get install samtools python3-deeptools - name: Start MongoDB v6.0 From 4d546260caf9d40b73d3f79201abe2217446675b Mon Sep 17 00:00:00 2001 From: Juanfe Sanahuja <85166064+juanfeSanahuja@users.noreply.github.com> Date: Fri, 21 Apr 2023 17:06:30 +0200 Subject: [PATCH 025/109] Update test-analysis.yml --- .github/workflows/test-analysis.yml | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index 2a96ffc4ffc..01cbc7d3d3d 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -42,18 +42,17 @@ jobs: run: mvn -T 2 clean install -P storage-hadoop,hdp3.1,${{ inputs.test_profile }} -DskipTests -Dcheckstyle.skip org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=opencb_opencga test: name: Execute JUnit and Jacoco tests - #runs-on: ubuntu-22.04 - runs-on: self-hosted + runs-on: ubuntu-22.04 steps: - uses: actions/checkout@v3 with: fetch-depth: '0' - #- name: Set up JDK 8 - # uses: actions/setup-java@v3 - # with: - # distribution: 'temurin' - # java-version: '8' - # cache: 'maven' + - name: Set up JDK 8 + uses: actions/setup-java@v3 + with: + distribution: 'temurin' + java-version: '8' + cache: 'maven' - name: Install Samtools run: sudo apt-get install samtools python3-deeptools - name: Start MongoDB v6.0 From df611903fdf5f2c24d6889114d23e6fd5b2e879b Mon Sep 17 00:00:00 2001 From: imedina Date: Tue, 25 Apr 2023 02:16:56 +0100 Subject: [PATCH 026/109] core: rename GitRepositoryState.get() to GitRepositoryState.getInstance() --- .../analysis/clinical/InterpretationAnalysis.java | 8 ++++---- .../exomiser/ExomiserInterpretationAnalysis.java | 4 ++-- .../circos/CircosLocalAnalysisExecutor.java | 2 +- .../GenomePlotLocalAnalysisExecutor.java | 2 +- .../hrdetect/HRDetectLocalAnalysisExecutor.java | 14 +------------- .../MutationalSignatureLocalAnalysisExecutor.java | 2 +- .../executors/DockerWrapperAnalysisExecutor.java | 2 +- .../analysis/rga/RgaSolrExtenalResource.java | 6 ++---- .../app/cli/admin/AdminCliOptionsParser.java | 4 ++-- .../opencb/opencga/app/cli/admin/AdminMain.java | 6 +++--- .../admin/executors/MigrationCommandExecutor.java | 2 +- .../app/cli/internal/InternalCliOptionsParser.java | 4 ++-- .../opencga/app/cli/internal/InternalMain.java | 6 +++--- .../app/cli/main/utils/CommandLineUtils.java | 12 ++++++------ .../opencga/app/cli/main/utils/JobsTopManager.java | 2 +- .../opencga/app/cli/session/SessionManager.java | 2 +- .../issue_1849/CompleteStatusDataModelUtils.java | 4 ++-- .../catalog/db/mongodb/MetaMongoDBAdaptor.java | 2 +- .../opencga/catalog/managers/AuditManager.java | 2 +- .../catalog/stats/solr/CatalogSolrManager.java | 2 +- .../opencga/catalog/templates/TemplateManager.java | 2 +- .../opencga/catalog/utils/PedigreeGraphUtils.java | 2 +- .../catalog/stats/solr/SolrExternalResource.java | 2 +- .../opencga/core/common/GitRepositoryState.java | 12 ++++++++++-- .../org/opencb/opencga/core/docs/DocBuilder.java | 2 +- .../org/opencb/opencga/core/models/Metadata.java | 2 +- .../opencga/core/models/common/InternalStatus.java | 4 ++-- .../opencb/opencga/core/tools/result/Status.java | 4 ++-- .../opencga/server/generator/models/RestApi.java | 2 +- .../opencb/opencga/server/rest/MetaWSServer.java | 6 +++--- .../opencga/server/rest/OpenCGAWSServer.java | 8 ++++---- .../main/resources/parserAbstractMethods.template | 4 ++-- .../opencga/storage/app/StorageAdminMain.java | 4 ++-- .../opencb/opencga/storage/app/StorageMain.java | 6 +++--- .../app/cli/client/ClientCliOptionsParser.java | 4 ++-- .../app/cli/server/AdminCliOptionsParser.java | 4 ++-- .../core/metadata/VariantMetadataConverter.java | 2 +- .../variant/solr/VariantSolrExternalResource.java | 2 +- .../hadoop/variant/executors/MRExecutor.java | 2 +- .../org/opencb/opencga/test/cli/OptionsParser.java | 4 ++-- 40 files changed, 80 insertions(+), 86 deletions(-) diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/InterpretationAnalysis.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/InterpretationAnalysis.java index 02ab7d9b5d8..4fe57ad701b 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/InterpretationAnalysis.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/InterpretationAnalysis.java @@ -79,8 +79,8 @@ protected InterpretationMethod getInterpretationMethod(String name) { .setName(name) .setDependencies(Collections.singletonList(new Software() .setName("OpenCGA") - .setVersion(GitRepositoryState.get().getBuildVersion()) - .setCommit(GitRepositoryState.get().getCommitId()))); + .setVersion(GitRepositoryState.getInstance().getBuildVersion()) + .setCommit(GitRepositoryState.getInstance().getCommitId()))); return method; } @@ -114,8 +114,8 @@ protected void saveInterpretation(String studyId, ClinicalAnalysis clinicalAnaly // Interpretation method InterpretationMethod method = new InterpretationMethod(getId(), null, null, - Collections.singletonList(new Software().setName("OpenCGA").setVersion(GitRepositoryState.get().getBuildVersion()) - .setCommit(GitRepositoryState.get().getCommitId()))); + Collections.singletonList(new Software().setName("OpenCGA").setVersion(GitRepositoryState.getInstance().getBuildVersion()) + .setCommit(GitRepositoryState.getInstance().getCommitId()))); // Analyst ClinicalAnalyst analyst = clinicalInterpretationManager.getAnalyst(token); diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysis.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysis.java index 07e35a78504..39fa4fd581c 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysis.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysis.java @@ -137,8 +137,8 @@ protected void run() throws ToolException { protected void saveInterpretation(String studyId, ClinicalAnalysis clinicalAnalysis) throws ToolException, StorageEngineException, CatalogException, IOException { // Interpretation method - InterpretationMethod method = new InterpretationMethod(getId(), GitRepositoryState.get().getBuildVersion(), - GitRepositoryState.get().getCommitId(), Collections.singletonList( + InterpretationMethod method = new InterpretationMethod(getId(), GitRepositoryState.getInstance().getBuildVersion(), + GitRepositoryState.getInstance().getCommitId(), Collections.singletonList( new Software() .setName("Exomiser") .setRepository("Docker: " + ExomiserWrapperAnalysisExecutor.DOCKER_IMAGE_NAME) diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/circos/CircosLocalAnalysisExecutor.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/circos/CircosLocalAnalysisExecutor.java index cd2ada565fa..40f829ecd6c 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/circos/CircosLocalAnalysisExecutor.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/circos/CircosLocalAnalysisExecutor.java @@ -58,7 +58,7 @@ public class CircosLocalAnalysisExecutor extends CircosAnalysisExecutor implements StorageToolExecutor { public final static String R_DOCKER_IMAGE = "opencb/opencga-ext-tools:" - + GitRepositoryState.get().getBuildVersion(); + + GitRepositoryState.getInstance().getBuildVersion(); private VariantStorageManager storageManager; private File snvsFile; diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/genomePlot/GenomePlotLocalAnalysisExecutor.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/genomePlot/GenomePlotLocalAnalysisExecutor.java index 027bb8dc9a8..4246e142d55 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/genomePlot/GenomePlotLocalAnalysisExecutor.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/genomePlot/GenomePlotLocalAnalysisExecutor.java @@ -61,7 +61,7 @@ public class GenomePlotLocalAnalysisExecutor extends GenomePlotAnalysisExecutor implements StorageToolExecutor { public final static String R_DOCKER_IMAGE = "opencb/opencga-ext-tools:" - + GitRepositoryState.get().getBuildVersion(); + + GitRepositoryState.getInstance().getBuildVersion(); private GenomePlotConfig plotConfig; diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/hrdetect/HRDetectLocalAnalysisExecutor.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/hrdetect/HRDetectLocalAnalysisExecutor.java index 4c96ad7b3b0..f85e0a1873a 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/hrdetect/HRDetectLocalAnalysisExecutor.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/hrdetect/HRDetectLocalAnalysisExecutor.java @@ -16,31 +16,21 @@ package org.opencb.opencga.analysis.variant.hrdetect; -import htsjdk.samtools.reference.BlockCompressedIndexedFastaSequenceFile; -import htsjdk.samtools.reference.FastaSequenceIndex; -import htsjdk.samtools.reference.ReferenceSequence; -import htsjdk.samtools.util.GZIIndex; import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.lang3.StringUtils; import org.opencb.biodata.models.variant.StudyEntry; import org.opencb.biodata.models.variant.Variant; -import org.opencb.biodata.models.variant.avro.VariantType; import org.opencb.commons.datastore.core.Query; import org.opencb.commons.datastore.core.QueryOptions; -import org.opencb.commons.datastore.core.QueryResultWriter; import org.opencb.commons.exec.Command; import org.opencb.commons.utils.DockerUtils; -import org.opencb.opencga.analysis.ResourceUtils; import org.opencb.opencga.analysis.StorageToolExecutor; import org.opencb.opencga.catalog.exceptions.CatalogException; import org.opencb.opencga.core.common.GitRepositoryState; import org.opencb.opencga.core.exceptions.ToolException; import org.opencb.opencga.core.exceptions.ToolExecutorException; -import org.opencb.opencga.core.response.OpenCGAResult; -import org.opencb.opencga.core.response.VariantQueryResult; import org.opencb.opencga.core.tools.annotations.ToolExecutor; import org.opencb.opencga.core.tools.variant.HRDetectAnalysisExecutor; -import org.opencb.opencga.core.tools.variant.MutationalSignatureAnalysisExecutor; import org.opencb.opencga.storage.core.exceptions.StorageEngineException; import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryParam; import org.opencb.opencga.storage.core.variant.adaptors.iterators.VariantDBIterator; @@ -53,14 +43,12 @@ import java.nio.file.Paths; import java.util.*; -import static org.opencb.opencga.analysis.variant.mutationalSignature.MutationalSignatureAnalysis.CATALOGUES_FILENAME_DEFAULT; - @ToolExecutor(id="opencga-local", tool = HRDetectAnalysis.ID, framework = ToolExecutor.Framework.LOCAL, source = ToolExecutor.Source.STORAGE) public class HRDetectLocalAnalysisExecutor extends HRDetectAnalysisExecutor implements StorageToolExecutor { - public final static String R_DOCKER_IMAGE = "opencb/opencga-ext-tools:" + GitRepositoryState.get().getBuildVersion(); + public final static String R_DOCKER_IMAGE = "opencb/opencga-ext-tools:" + GitRepositoryState.getInstance().getBuildVersion(); private final static String CNV_FILENAME = "cnv.tsv"; private final static String INDEL_FILENAME = "indel.vcf"; diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/mutationalSignature/MutationalSignatureLocalAnalysisExecutor.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/mutationalSignature/MutationalSignatureLocalAnalysisExecutor.java index 55173c3bd3a..d0b17eac64a 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/mutationalSignature/MutationalSignatureLocalAnalysisExecutor.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/mutationalSignature/MutationalSignatureLocalAnalysisExecutor.java @@ -65,7 +65,7 @@ public class MutationalSignatureLocalAnalysisExecutor extends MutationalSignatur implements StorageToolExecutor { public final static String R_DOCKER_IMAGE = "opencb/opencga-ext-tools:" - + GitRepositoryState.get().getBuildVersion(); + + GitRepositoryState.getInstance().getBuildVersion(); private Path opencgaHome; diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/executors/DockerWrapperAnalysisExecutor.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/executors/DockerWrapperAnalysisExecutor.java index 27d6c54d7b3..21f619cc5a4 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/executors/DockerWrapperAnalysisExecutor.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/wrappers/executors/DockerWrapperAnalysisExecutor.java @@ -32,7 +32,7 @@ public String getDockerImageName() { } public String getDockerImageVersion() { - return GitRepositoryState.get().getBuildVersion(); + return GitRepositoryState.getInstance().getBuildVersion(); } private Logger privateLogger = LoggerFactory.getLogger(DockerWrapperAnalysisExecutor.class); diff --git a/opencga-analysis/src/test/java/org/opencb/opencga/analysis/rga/RgaSolrExtenalResource.java b/opencga-analysis/src/test/java/org/opencb/opencga/analysis/rga/RgaSolrExtenalResource.java index 0884482ef80..f45e8e77ec2 100644 --- a/opencga-analysis/src/test/java/org/opencb/opencga/analysis/rga/RgaSolrExtenalResource.java +++ b/opencga-analysis/src/test/java/org/opencb/opencga/analysis/rga/RgaSolrExtenalResource.java @@ -5,10 +5,8 @@ import org.apache.solr.client.solrj.SolrServerException; import org.apache.solr.client.solrj.embedded.EmbeddedSolrServer; import org.apache.solr.core.NodeConfig; -import org.apache.solr.core.SolrResourceLoader; import org.junit.rules.ExternalResource; import org.opencb.commons.datastore.solr.SolrManager; -import org.opencb.opencga.analysis.variant.manager.VariantStorageManager; import org.opencb.opencga.core.common.GitRepositoryState; import org.opencb.opencga.core.config.storage.StorageConfiguration; @@ -40,8 +38,8 @@ protected void before() throws Throwable { Path rootDir = getTmpRootDir(); - String mainConfigSet = "opencga-rga-configset-" + GitRepositoryState.get().getBuildVersion(); - String auxConfigSet = "opencga-rga-aux-configset-" + GitRepositoryState.get().getBuildVersion(); + String mainConfigSet = "opencga-rga-configset-" + GitRepositoryState.getInstance().getBuildVersion(); + String auxConfigSet = "opencga-rga-aux-configset-" + GitRepositoryState.getInstance().getBuildVersion(); copyConfigSetConfiguration(mainConfigSet, "managed-schema"); copyConfigSetConfiguration(auxConfigSet, "aux-managed-schema"); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/AdminCliOptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/AdminCliOptionsParser.java index 89832e53260..28787847b65 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/AdminCliOptionsParser.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/AdminCliOptionsParser.java @@ -800,8 +800,8 @@ public void printUsage() { if (parsedCommand.isEmpty()) { System.err.println(""); System.err.println("Program: OpenCGA Admin (OpenCB)"); - System.err.println("Version: " + GitRepositoryState.get().getBuildVersion()); - System.err.println("Git commit: " + GitRepositoryState.get().getCommitId()); + System.err.println("Version: " + GitRepositoryState.getInstance().getBuildVersion()); + System.err.println("Git commit: " + GitRepositoryState.getInstance().getCommitId()); System.err.println("Description: Big Data platform for processing and analysing NGS data"); System.err.println(""); System.err.println("Usage: opencga-admin.sh [-h|--help] [--version] [options]"); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/AdminMain.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/AdminMain.java index 2bb78fb51c3..2dc1f8d638b 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/AdminMain.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/AdminMain.java @@ -30,7 +30,7 @@ */ public class AdminMain { - public static final String VERSION = GitRepositoryState.get().getBuildVersion(); + public static final String VERSION = GitRepositoryState.getInstance().getBuildVersion(); public static void main(String[] args) { @@ -71,8 +71,8 @@ public static void main(String[] args) { String parsedCommand = cliOptionsParser.getCommand(); if (parsedCommand == null || parsedCommand.isEmpty()) { if (cliOptionsParser.getGeneralOptions().version) { - System.out.println("Version " + GitRepositoryState.get().getBuildVersion()); - System.out.println("Git version: " + GitRepositoryState.get().getBranch() + " " + GitRepositoryState.get().getCommitId()); + System.out.println("Version " + GitRepositoryState.getInstance().getBuildVersion()); + System.out.println("Git version: " + GitRepositoryState.getInstance().getBranch() + " " + GitRepositoryState.getInstance().getCommitId()); System.exit(0); } else if (cliOptionsParser.getGeneralOptions().help) { cliOptionsParser.printUsage(); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/executors/MigrationCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/executors/MigrationCommandExecutor.java index ceaab6ea98d..a360eaa2f1e 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/executors/MigrationCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/admin/executors/MigrationCommandExecutor.java @@ -167,7 +167,7 @@ private String parseVersion(String version) { public static String getDefaultVersion() { String version; - version = GitRepositoryState.get().getBuildVersion(); + version = GitRepositoryState.getInstance().getBuildVersion(); // Remove extra information version = version.split("-")[0]; return version; diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/InternalCliOptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/InternalCliOptionsParser.java index f11d519c846..132ad854c82 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/InternalCliOptionsParser.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/InternalCliOptionsParser.java @@ -468,8 +468,8 @@ public void printUsage() { if (parsedCommand.isEmpty()) { System.err.println(""); System.err.println("Program: OpenCGA Analysis (OpenCB)"); - System.err.println("Version: " + GitRepositoryState.get().getBuildVersion()); - System.err.println("Git commit: " + GitRepositoryState.get().getCommitId()); + System.err.println("Version: " + GitRepositoryState.getInstance().getBuildVersion()); + System.err.println("Git commit: " + GitRepositoryState.getInstance().getCommitId()); System.err.println("Description: Big Data platform for processing and analysing NGS data"); System.err.println(""); System.err.println("Usage: opencga-internal.sh [-h|--help] [--version] [options]"); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/InternalMain.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/InternalMain.java index a1aaf7466f3..98d8b965357 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/InternalMain.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/InternalMain.java @@ -28,7 +28,7 @@ */ public class InternalMain { - public static final String VERSION = GitRepositoryState.get().getBuildVersion(); + public static final String VERSION = GitRepositoryState.getInstance().getBuildVersion(); public static void main(String[] args) { System.exit(privateMain(args)); @@ -48,8 +48,8 @@ public static int privateMain(String[] args) { String parsedCommand = cliOptionsParser.getCommand(); if (parsedCommand == null || parsedCommand.isEmpty()) { if (cliOptionsParser.getGeneralOptions().version) { - System.out.println("Version " + GitRepositoryState.get().getBuildVersion()); - System.out.println("Git version: " + GitRepositoryState.get().getBranch() + " " + GitRepositoryState.get().getCommitId()); + System.out.println("Version " + GitRepositoryState.getInstance().getBuildVersion()); + System.out.println("Git version: " + GitRepositoryState.getInstance().getBranch() + " " + GitRepositoryState.getInstance().getCommitId()); return 0; } else if (cliOptionsParser.getGeneralOptions().help) { cliOptionsParser.printUsage(); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/utils/CommandLineUtils.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/utils/CommandLineUtils.java index 46af3e8eeb9..4454887584b 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/utils/CommandLineUtils.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/utils/CommandLineUtils.java @@ -18,16 +18,16 @@ public class CommandLineUtils { private static final Logger logger = LoggerFactory.getLogger(CommandLineUtils.class); public static String getVersionString() { - String res = PrintUtils.getKeyValueAsFormattedString("\tOpenCGA CLI version: ", "\t" + GitRepositoryState.get().getBuildVersion() + "\n"); - res += PrintUtils.getKeyValueAsFormattedString("\tGit version:", "\t\t" + GitRepositoryState.get().getBranch() + " " + GitRepositoryState.get().getCommitId() + "\n"); + String res = PrintUtils.getKeyValueAsFormattedString("\tOpenCGA CLI version: ", "\t" + GitRepositoryState.getInstance().getBuildVersion() + "\n"); + res += PrintUtils.getKeyValueAsFormattedString("\tGit version:", "\t\t" + GitRepositoryState.getInstance().getBranch() + " " + GitRepositoryState.getInstance().getCommitId() + "\n"); res += PrintUtils.getKeyValueAsFormattedString("\tProgram:", "\t\tOpenCGA (OpenCB)" + "\n"); res += PrintUtils.getKeyValueAsFormattedString("\tDescription: ", "\t\tBig Data platform for processing and analysing NGS data" + "\n"); return res; } public static String getHelpVersionString() { - String res = PrintUtils.getHelpVersionFormattedString("OpenCGA CLI version: ", "\t" + GitRepositoryState.get().getBuildVersion() + "\n"); - res += PrintUtils.getHelpVersionFormattedString("Git version:", "\t\t" + GitRepositoryState.get().getBranch() + " " + GitRepositoryState.get().getCommitId() + "\n"); + String res = PrintUtils.getHelpVersionFormattedString("OpenCGA CLI version: ", "\t" + GitRepositoryState.getInstance().getBuildVersion() + "\n"); + res += PrintUtils.getHelpVersionFormattedString("Git version:", "\t\t" + GitRepositoryState.getInstance().getBranch() + " " + GitRepositoryState.getInstance().getCommitId() + "\n"); res += PrintUtils.getHelpVersionFormattedString("Program:", "\t\tOpenCGA (OpenCB)" + "\n"); res += PrintUtils.getHelpVersionFormattedString("Description: ", "\t\tBig Data platform for processing and analysing NGS data" + "\n"); return res; @@ -90,7 +90,7 @@ public static String[] processShortCuts(String[] args) { break; case "--build-version": case "build-version": - println(GitRepositoryState.get().getBuildVersion()); + println(GitRepositoryState.getInstance().getBuildVersion()); break; case "logout": return ArrayUtils.addAll(new String[]{"users"}, args); @@ -99,7 +99,7 @@ public static String[] processShortCuts(String[] args) { if (args.length > 1 && args[1].equals("studies")) { println(String.join(", ", OpencgaMain.getShell().getSessionManager().getSession().getStudies()), Color.GREEN); } else { - printWarn("Opencga version " + GitRepositoryState.get().getBuildVersion() + " can only list studies"); + printWarn("Opencga version " + GitRepositoryState.getInstance().getBuildVersion() + " can only list studies"); } } else { printWarn("List studies is only available in Shell mode"); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/utils/JobsTopManager.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/utils/JobsTopManager.java index 1c2099ec471..15d7b63e6ec 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/utils/JobsTopManager.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/utils/JobsTopManager.java @@ -150,7 +150,7 @@ public void print(JobTop top) { jobTable.restoreCursorPosition(); jobTable.println("OpenCGA jobs TOP"); - jobTable.println(" Version " + GitRepositoryState.get().getBuildVersion()); + jobTable.println(" Version " + GitRepositoryState.getInstance().getBuildVersion()); jobTable.println(" " + TextOutputWriter.SIMPLE_DATE_FORMAT.format(Date.from(Instant.now()))); jobTable.println(); jobTable.print(Enums.ExecutionStatus.RUNNING + ": " + top.getStats().getRunning() + ", "); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/session/SessionManager.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/session/SessionManager.java index 640a687f7c3..f822716041e 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/session/SessionManager.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/session/SessionManager.java @@ -111,7 +111,7 @@ private void init() { private Session createEmptySession() { Session session = new Session(); session.setHost(host); - session.setVersion(GitRepositoryState.get().getBuildVersion()); + session.setVersion(GitRepositoryState.getInstance().getBuildVersion()); session.setTimestamp(System.currentTimeMillis()); session.setStudies(new ArrayList()); session.setCurrentStudy(NO_STUDY); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_2_0/catalog/issue_1849/CompleteStatusDataModelUtils.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_2_0/catalog/issue_1849/CompleteStatusDataModelUtils.java index d23d2345681..d9e270c3d9f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_2_0/catalog/issue_1849/CompleteStatusDataModelUtils.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_2_0/catalog/issue_1849/CompleteStatusDataModelUtils.java @@ -35,8 +35,8 @@ public static void completeInternalStatus(Document document) { completeStatus(internal); Document status = internal.get("status", Document.class); - status.put("version", GitRepositoryState.get().getBuildVersion()); - status.put("commit", GitRepositoryState.get().getCommitId()); + status.put("version", GitRepositoryState.getInstance().getBuildVersion()); + status.put("commit", GitRepositoryState.getInstance().getCommitId()); String id = status.getString("id"); if (StringUtils.isEmpty(id)) { diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/MetaMongoDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/MetaMongoDBAdaptor.java index 1a98f5a99a9..9fc90a7b621 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/MetaMongoDBAdaptor.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/MetaMongoDBAdaptor.java @@ -55,7 +55,7 @@ public class MetaMongoDBAdaptor extends MongoDBAdaptor implements MetaDBAdaptor Filters.eq(ID, MongoDBAdaptorFactory.METADATA_OBJECT_ID), Filters.eq(OLD_ID, MongoDBAdaptorFactory.METADATA_OBJECT_ID)); private final MongoDBCollection metaCollection; - private static final String VERSION = GitRepositoryState.get().getBuildVersion(); + private static final String VERSION = GitRepositoryState.getInstance().getBuildVersion(); public MetaMongoDBAdaptor(MongoDBCollection metaMongoDBCollection, Configuration configuration, MongoDBAdaptorFactory dbAdaptorFactory) { diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/AuditManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/AuditManager.java index 1f0a9ae40c6..b95d3b0ff0e 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/AuditManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/AuditManager.java @@ -184,7 +184,7 @@ public void audit(String operationId, String userId, Enums.Action action, Enums. public void audit(String operationId, String userId, Enums.Action action, Enums.Resource resource, String resourceId, String resourceUuid, String studyId, String studyUuid, ObjectMap params, AuditRecord.Status status, ObjectMap attributes) { - String apiVersion = GitRepositoryState.get().getBuildVersion(); + String apiVersion = GitRepositoryState.getInstance().getBuildVersion(); Date date = TimeUtils.getDate(); String auditId = UuidUtils.generateOpenCgaUuid(UuidUtils.Entity.AUDIT); diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/stats/solr/CatalogSolrManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/stats/solr/CatalogSolrManager.java index 6be7ad1be28..b1c2df87d1f 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/stats/solr/CatalogSolrManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/stats/solr/CatalogSolrManager.java @@ -268,7 +268,7 @@ public DataResult facetedQuery(Study study, String collection, Query //***************** PRIVATE ****************/ private void populateConfigCollectionMap() { - String version = GitRepositoryState.get().getBuildVersion(); + String version = GitRepositoryState.getInstance().getBuildVersion(); CONFIGS_COLLECTION.put(DATABASE_PREFIX + COHORT_SOLR_COLLECTION, COHORT_CONF_SET + "-" + version); CONFIGS_COLLECTION.put(DATABASE_PREFIX + FILE_SOLR_COLLECTION, FILE_CONF_SET + "-" + version); diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/templates/TemplateManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/templates/TemplateManager.java index 16a638e0e2d..bb59584363b 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/templates/TemplateManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/templates/TemplateManager.java @@ -125,7 +125,7 @@ public void validate(TemplateManifest manifest) throws CatalogException { } // Check version - GitRepositoryState gitRepositoryState = GitRepositoryState.get(); + GitRepositoryState gitRepositoryState = GitRepositoryState.getInstance(); String version = gitRepositoryState.getBuildVersion(); String versionShort; if (version.contains("-")) { diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/utils/PedigreeGraphUtils.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/utils/PedigreeGraphUtils.java index 9da89bab416..62394a6e562 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/utils/PedigreeGraphUtils.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/utils/PedigreeGraphUtils.java @@ -25,7 +25,7 @@ public class PedigreeGraphUtils { public static final String PEDIGREE_JSON_FILENAME = "ped_coords.json"; public static final String PEDIGREE_TSV_FILENAME = "ped_coords.tsv"; - public static final String R_DOCKER_IMAGE = "opencb/opencga-ext-tools:" + GitRepositoryState.get().getBuildVersion(); + public static final String R_DOCKER_IMAGE = "opencb/opencga-ext-tools:" + GitRepositoryState.getInstance().getBuildVersion(); public static PedigreeGraph getPedigreeGraph(Family family, Path openCgaHome, Path scratchDir) throws IOException { PedigreeGraph pedigreeGraph = new PedigreeGraph(); diff --git a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/stats/solr/SolrExternalResource.java b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/stats/solr/SolrExternalResource.java index cc0a758e602..677262d5cf8 100644 --- a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/stats/solr/SolrExternalResource.java +++ b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/stats/solr/SolrExternalResource.java @@ -41,7 +41,7 @@ public void before() throws Exception { Path rootDir = getOpencgaHome(); - String version = GitRepositoryState.get().getBuildVersion(); + String version = GitRepositoryState.getInstance().getBuildVersion(); // Copy configuration copyConfiguration("cohort-managed-schema", CatalogSolrManager.COHORT_CONF_SET + "-" + version); diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/common/GitRepositoryState.java b/opencga-core/src/main/java/org/opencb/opencga/core/common/GitRepositoryState.java index 80f1563dec6..790d8adcbe0 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/common/GitRepositoryState.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/common/GitRepositoryState.java @@ -32,6 +32,7 @@ public class GitRepositoryState { public static final String DEFAULT_RESOURCE_NAME = "git.properties"; private static GitRepositoryState gitRepositoryState; + private static Properties properties; private static final Logger logger = LoggerFactory.getLogger(GitRepositoryState.class); private String tags; // =${git.tags} // comma separated tag names @@ -57,9 +58,16 @@ public class GitRepositoryState { private String buildHost; // =${git.build.host} private String buildVersion; // =${git.build.version} - public static GitRepositoryState get() { + public static String get(String key) { + if (properties == null) { + getInstance(); + } + return properties.getProperty(key); + } + + public static GitRepositoryState getInstance() { if (gitRepositoryState == null) { - Properties properties = new Properties(); + properties = new Properties(); InputStream stream = null; try { stream = GitRepositoryState.class.getClassLoader().getResourceAsStream(DEFAULT_RESOURCE_NAME); diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/docs/DocBuilder.java b/opencga-core/src/main/java/org/opencb/opencga/core/docs/DocBuilder.java index 53f0014dd27..a647bbd8b43 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/docs/DocBuilder.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/docs/DocBuilder.java @@ -44,7 +44,7 @@ public static void main(String[] args) { config.setType(DocFactory.DocFactoryType.MARKDOWN); config.setOutputDir("/workspace/opencga/docs/data-models/"); config.setGithubServerURL("https://github.com/opencb/opencga/tree/" - + GitRepositoryState.get().getBranch() + "/opencga-core"); + + GitRepositoryState.getInstance().getBranch() + "/opencga-core"); config.setJsondir("/workspace/opencga/opencga-core/src/main/resources/doc/json"); config.setGitbookServerURL("https://docs.opencga.opencb.org/data-models"); try { diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/Metadata.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/Metadata.java index a0a67ee823a..99fb1bedeaa 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/models/Metadata.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/models/Metadata.java @@ -31,7 +31,7 @@ public class Metadata { public Metadata() { - this(GitRepositoryState.get().getBuildVersion(), TimeUtils.getTime()); + this(GitRepositoryState.getInstance().getBuildVersion(), TimeUtils.getTime()); } public Metadata(String version, String creationDate) { diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/common/InternalStatus.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/common/InternalStatus.java index 732cb04adaf..a934efdc3ee 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/models/common/InternalStatus.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/models/common/InternalStatus.java @@ -120,8 +120,8 @@ protected void init(String statusId, String statusName, String description) { super.name = statusName; super.description = description; super.date = TimeUtils.getTime(); - this.version = GitRepositoryState.get().getBuildVersion(); - this.commit = GitRepositoryState.get().getCommitId(); + this.version = GitRepositoryState.getInstance().getBuildVersion(); + this.commit = GitRepositoryState.getInstance().getCommitId(); } @Override diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/tools/result/Status.java b/opencga-core/src/main/java/org/opencb/opencga/core/tools/result/Status.java index da1778bf650..dc811356a1a 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/tools/result/Status.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/tools/result/Status.java @@ -61,8 +61,8 @@ public Status(Type name, String step, Date date) { public static Status initStatus() { Status status = new Status(); - status.version = GitRepositoryState.get().getBuildVersion(); - status.commit = GitRepositoryState.get().getCommitId(); + status.version = GitRepositoryState.getInstance().getBuildVersion(); + status.commit = GitRepositoryState.getInstance().getCommitId(); return status; } diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/generator/models/RestApi.java b/opencga-server/src/main/java/org/opencb/opencga/server/generator/models/RestApi.java index 84ae7f75aae..cff66f13e62 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/generator/models/RestApi.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/generator/models/RestApi.java @@ -28,7 +28,7 @@ public class RestApi { private List categories; public RestApi() { - this(GitRepositoryState.get().getBuildVersion(), GitRepositoryState.get().getCommitId(), new ArrayList<>()); + this(GitRepositoryState.getInstance().getBuildVersion(), GitRepositoryState.getInstance().getCommitId(), new ArrayList<>()); } public RestApi(String version, String commit, List categories) { diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/rest/MetaWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/rest/MetaWSServer.java index e075e938983..528853faeb6 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/rest/MetaWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/rest/MetaWSServer.java @@ -80,9 +80,9 @@ public MetaWSServer(@Context UriInfo uriInfo, @Context HttpServletRequest httpSe public Response getAbout() { Map info = new HashMap<>(5); info.put("Program", "OpenCGA (OpenCB)"); - info.put("Version", GitRepositoryState.get().getBuildVersion()); - info.put("Git branch", GitRepositoryState.get().getBranch()); - info.put("Git commit", GitRepositoryState.get().getCommitId()); + info.put("Version", GitRepositoryState.getInstance().getBuildVersion()); + info.put("Git branch", GitRepositoryState.getInstance().getBranch()); + info.put("Git commit", GitRepositoryState.getInstance().getCommitId()); info.put("Description", "Big Data platform for processing and analysing NGS data"); OpenCGAResult queryResult = new OpenCGAResult(); queryResult.setTime(0); diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/rest/OpenCGAWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/rest/OpenCGAWSServer.java index d152cf17277..03a39102d9e 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/rest/OpenCGAWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/rest/OpenCGAWSServer.java @@ -260,8 +260,8 @@ static void init(String opencgaHomeStr) { } logger.info("| OpenCGA REST successfully started!"); - logger.info("| - Version " + GitRepositoryState.get().getBuildVersion()); - logger.info("| - Git version: " + GitRepositoryState.get().getBranch() + " " + GitRepositoryState.get().getCommitId()); + logger.info("| - Version " + GitRepositoryState.getInstance().getBuildVersion()); + logger.info("| - Git version: " + GitRepositoryState.getInstance().getBranch() + " " + GitRepositoryState.getInstance().getCommitId()); logger.info("========================================================================\n"); } @@ -428,8 +428,8 @@ private static void addErrorEvent(RestResponse response, Throwable e) { } public static void setFederationServer(OpenCGAResult result, String baseuri) { - result.setFederationNode(new FederationNode(baseuri, GitRepositoryState.get().getCommitId(), - GitRepositoryState.get().getBuildVersion())); + result.setFederationNode(new FederationNode(baseuri, GitRepositoryState.getInstance().getCommitId(), + GitRepositoryState.getInstance().getBuildVersion())); } public static void logResponse(Response.StatusType statusInfo, RestResponse queryResponse, long startTime, diff --git a/opencga-server/src/main/resources/parserAbstractMethods.template b/opencga-server/src/main/resources/parserAbstractMethods.template index a06cc76c2f1..4d25b76e871 100644 --- a/opencga-server/src/main/resources/parserAbstractMethods.template +++ b/opencga-server/src/main/resources/parserAbstractMethods.template @@ -18,8 +18,8 @@ if (parsedCommand.isEmpty()) { System.err.println(""); System.err.println("Program: OpenCGA (OpenCB)"); - System.err.println("Version: " + GitRepositoryState.get().getBuildVersion()); - System.err.println("Git commit: " + GitRepositoryState.get().getCommitId()); + System.err.println("Version: " + GitRepositoryState.getInstance().getBuildVersion()); + System.err.println("Git commit: " + GitRepositoryState.getInstance().getCommitId()); System.err.println("Description: Big Data platform for processing and analysing NGS data"); System.err.println(""); System.err.println("Usage: opencga.sh [-h|--help] [--version] [options]"); diff --git a/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/StorageAdminMain.java b/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/StorageAdminMain.java index 85313d4e4c3..0825354d734 100644 --- a/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/StorageAdminMain.java +++ b/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/StorageAdminMain.java @@ -48,8 +48,8 @@ public static int privateMain(String[] args) { String parsedCommand = adminCliOptionsParser.getCommand(); if (parsedCommand == null || parsedCommand.isEmpty()) { if (adminCliOptionsParser.getGeneralOptions().version) { - System.out.println("Version " + GitRepositoryState.get().getBuildVersion()); - System.out.println("Git version: " + GitRepositoryState.get().getBranch() + " " + GitRepositoryState.get().getCommitId()); + System.out.println("Version " + GitRepositoryState.getInstance().getBuildVersion()); + System.out.println("Git version: " + GitRepositoryState.getInstance().getBranch() + " " + GitRepositoryState.getInstance().getCommitId()); return 0; } else if (adminCliOptionsParser.getGeneralOptions().help) { adminCliOptionsParser.printUsage(); diff --git a/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/StorageMain.java b/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/StorageMain.java index 05da1e97637..9f7ec6fd321 100644 --- a/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/StorageMain.java +++ b/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/StorageMain.java @@ -48,9 +48,9 @@ public static int privateMain(String[] args) { String parsedCommand = cliOptionsParser.getCommand(); if (parsedCommand == null || parsedCommand.isEmpty()) { if (cliOptionsParser.getGeneralOptions().version) { - System.out.println("Version " + GitRepositoryState.get().getBuildVersion()); - System.out.println("Git version: " + GitRepositoryState.get().getBranch() + " " + GitRepositoryState.get().getCommitId()); -// System.out.println(GitRepositoryState.get()); + System.out.println("Version " + GitRepositoryState.getInstance().getBuildVersion()); + System.out.println("Git version: " + GitRepositoryState.getInstance().getBranch() + " " + GitRepositoryState.getInstance().getCommitId()); +// System.out.println(GitRepositoryState.getInstance()); return 0; } else if (cliOptionsParser.getGeneralOptions().help) { cliOptionsParser.printUsage(); diff --git a/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/cli/client/ClientCliOptionsParser.java b/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/cli/client/ClientCliOptionsParser.java index 9c430b284c1..fb567276992 100644 --- a/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/cli/client/ClientCliOptionsParser.java +++ b/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/cli/client/ClientCliOptionsParser.java @@ -82,8 +82,8 @@ public void printUsage() { if (parsedCommand.isEmpty()) { System.err.println(""); System.err.println("Program: OpenCGA Storage (OpenCB)"); - System.err.println("Version: " + GitRepositoryState.get().getBuildVersion()); - System.err.println("Git commit: " + GitRepositoryState.get().getCommitId()); + System.err.println("Version: " + GitRepositoryState.getInstance().getBuildVersion()); + System.err.println("Git commit: " + GitRepositoryState.getInstance().getCommitId()); System.err.println("Description: Big Data platform for processing and analysing NGS data"); System.err.println(""); System.err.println("Usage: opencga-storage.sh [-h|--help] [--version] [options]"); diff --git a/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/cli/server/AdminCliOptionsParser.java b/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/cli/server/AdminCliOptionsParser.java index 7aedfbd4e85..86a4bcca419 100644 --- a/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/cli/server/AdminCliOptionsParser.java +++ b/opencga-storage/opencga-storage-app/src/main/java/org/opencb/opencga/storage/app/cli/server/AdminCliOptionsParser.java @@ -76,8 +76,8 @@ public void printUsage() { if (parsedCommand.isEmpty()) { System.err.println(""); System.err.println("Program: OpenCGA Storage Admin (OpenCB)"); - System.err.println("Version: " + GitRepositoryState.get().getBuildVersion()); - System.err.println("Git commit: " + GitRepositoryState.get().getCommitId()); + System.err.println("Version: " + GitRepositoryState.getInstance().getBuildVersion()); + System.err.println("Git commit: " + GitRepositoryState.getInstance().getCommitId()); System.err.println("Description: Big Data platform for processing and analysing NGS data"); System.err.println(""); System.err.println("Usage: opencga-storage-admin.sh [-h|--help] [--version] [options]"); diff --git a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/metadata/VariantMetadataConverter.java b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/metadata/VariantMetadataConverter.java index 1ec92d91ea9..d2114731bc1 100644 --- a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/metadata/VariantMetadataConverter.java +++ b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/metadata/VariantMetadataConverter.java @@ -48,7 +48,7 @@ public VariantMetadata toVariantMetadata(VariantQueryProjection variantQueryProj // .setDate(Date.from(Instant.now()).toString()) .setCreationDate(TimeUtils.getTime()) .setStudies(studies) - .setVersion(GitRepositoryState.get().getDescribeShort()) + .setVersion(GitRepositoryState.getInstance().getDescribeShort()) .setSpecies(species) .build(); diff --git a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/solr/VariantSolrExternalResource.java b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/solr/VariantSolrExternalResource.java index 122ef2da4af..031360d3298 100644 --- a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/solr/VariantSolrExternalResource.java +++ b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/solr/VariantSolrExternalResource.java @@ -63,7 +63,7 @@ protected void before() throws Throwable { Path rootDir = getTmpRootDir(); - String configSet = "opencga-variant-configset-" + GitRepositoryState.get().getBuildVersion(); + String configSet = "opencga-variant-configset-" + GitRepositoryState.getInstance().getBuildVersion(); // Copy configuration getResourceUri("configsets/variantsCollection/solrconfig.xml", "configsets/" + configSet + "/solrconfig.xml"); diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/executors/MRExecutor.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/executors/MRExecutor.java index 7ba0a4faf85..ef8f97152ad 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/executors/MRExecutor.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/executors/MRExecutor.java @@ -51,7 +51,7 @@ public MRExecutor init(ObjectMap options) { public static String getJarWithDependencies(ObjectMap options) throws StorageEngineException { String jar = options.getString(MR_JAR_WITH_DEPENDENCIES.key(), null); if (jar == null) { - jar = "opencga-storage-hadoop-core-" + GitRepositoryState.get().getBuildVersion() + "-jar-with-dependencies.jar"; + jar = "opencga-storage-hadoop-core-" + GitRepositoryState.getInstance().getBuildVersion() + "-jar-with-dependencies.jar"; // throw new StorageEngineException("Missing option " + MR_JAR_WITH_DEPENDENCIES); } if (!Paths.get(jar).isAbsolute()) { diff --git a/opencga-test/src/main/java/org/opencb/opencga/test/cli/OptionsParser.java b/opencga-test/src/main/java/org/opencb/opencga/test/cli/OptionsParser.java index efd41c2b319..256df4315ee 100644 --- a/opencga-test/src/main/java/org/opencb/opencga/test/cli/OptionsParser.java +++ b/opencga-test/src/main/java/org/opencb/opencga/test/cli/OptionsParser.java @@ -76,8 +76,8 @@ public static void printVersion() { private static Map getVersionMap() { Map versionMap = new HashMap<>(); - versionMap.put("OpenCGA Test version:", GitRepositoryState.get().getBuildVersion()); - versionMap.put("Git version:", "" + GitRepositoryState.get().getBranch() + " " + GitRepositoryState.get().getCommitId()); + versionMap.put("OpenCGA Test version:", GitRepositoryState.getInstance().getBuildVersion()); + versionMap.put("Git version:", "" + GitRepositoryState.getInstance().getBranch() + " " + GitRepositoryState.getInstance().getCommitId()); versionMap.put("Program:", "OpenCGA-test (OpenCB)"); versionMap.put("Description:", "Data generation application for the openCGA platform"); return versionMap; From 1e5d4312515e1b9ed1b24e098f9fc1a84857050c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 4 May 2023 19:39:44 +0200 Subject: [PATCH 027/109] delete file misc/sync_dependency.sh no longer necessary #TASK-4163 --- misc/sync_dependency.sh | 145 ---------------------------------------- 1 file changed, 145 deletions(-) delete mode 100755 misc/sync_dependency.sh diff --git a/misc/sync_dependency.sh b/misc/sync_dependency.sh deleted file mode 100755 index 316bbc39d3b..00000000000 --- a/misc/sync_dependency.sh +++ /dev/null @@ -1,145 +0,0 @@ -#!/bin/bash - -function yellow (){ - echo "$(tput setaf 3)$1$(tput setaf 7)" -} -function green (){ - echo "$(tput setaf 2)$1$(tput setaf 7)" -} -function cyan (){ - echo "$(tput setaf 6)$1$(tput setaf 7)" -} - -function printUsage(){ - echo "" - yellow "Release an OpenCB project." - echo "" - echo "Usage: $(basename $0) --biodata|-b|--java-common-libs|-j" - echo "" - cyan "Options:" - green " -j --java-common-libs STRING Update java-common-libs dependency" - green " -b --biodata STRING Update biodata dependency" - echo "" -} - -## Check if the repo status is clean. -function check_repo_clean() { - GIT_STATUS=$(git status --short) - if [ -n "$GIT_STATUS" ]; then - yellow "Repository is not clean:" - yellow "$GIT_STATUS" - exit - fi -} - -## This function removes TASK-XXX- if exists, otherwise it adds it. -function toggle_version() { - local BRANCH=$1 - if [[ "$POM_DEPENDENCY_VERSION" == *"$BRANCH"* ]]; then - ## Remove TASK-XXX- from the current version - ## Example: remove 'TASK-1234-' from 2.6.0-TASK-1234-SNAPSHOT - NEW_VERSION=${POM_DEPENDENCY_VERSION/"$BRANCH-"} - else - ## Add 'TASK-XXX-' to the current version - ## Example: 2.6.0-SNAPSHOT --> 2.6.0-TASK-1234-SNAPSHOT - CLEAN_RELEASE_VERSION=$(echo "$POM_DEPENDENCY_VERSION" | cut -d "-" -f 1) - TAG_VERSION=$(echo "$POM_DEPENDENCY_VERSION" | cut -d "-" -f 2) - NEW_VERSION="$CLEAN_RELEASE_VERSION-$BRANCH-$TAG_VERSION" - fi -} - -## Change version in the dependency. -## Usage: update_dependency "$DEPENDENCY_REPO" "$NEW_VERSION" "$BRANCH_NAME" -function update_dependency() { - ## Save current directory - local pwd=$PWD - cd "$1" || exit 2 - check_repo_clean - git checkout "$3" - ## Check branch exists - local BRANCH=$(git branch --show-current) - if [ "$BRANCH" != "$3" ]; then - yellow "Branch '$3' does not exist" - exit - fi - ## Rename and commit new version - mvn versions:set -DnewVersion="$2" -DgenerateBackupPoms=false - git commit -am "Update version to $2" - ## Restore directory - cd "$pwd" || exit 2 -} - -## At least one parameter is required. -if [ -z "$1" ]; then - printUsage - exit 1 -fi - -while [[ $# -gt 0 ]]; do - key="$1" - if [ -n "$2" ]; then - DEPENDENCY_REPO="$2" - fi - case $key in - -h | --help) - printUsage - exit 0 - ;; - -j | --java-common-libs) - LIB="JAVA_COMMONS_LIB" - if [ -z "$DEPENDENCY_REPO" ]; then - DEPENDENCY_REPO="../java-common-libs" - else - shift - fi - shift # past argument - ;; - -b | --biodata) - LIB="BIODATA" - if [ -z "$DEPENDENCY_REPO" ]; then - DEPENDENCY_REPO="../biodata" - else - shift - fi - shift # past argument - ;; - *) # unknown option - echo "Unknown option $key" - printUsage - exit 1 - ;; - esac -done - -SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd ) -CURRENT_DIR=$PWD -cd "$SCRIPT_DIR" || exit 2 -cd .. -BRANCH_NAME=$(git branch --show-current) -if [[ "$BRANCH_NAME" == "TASK-"* ]]; then - check_repo_clean "$BRANCH_NAME" -else - yellow "[$BRANCH_NAME] The branch name must start with TASK-" - yellow "$GIT_STATUS" - exit -fi - -function update_library(){ - local LIBRARY="$1" - POM_DEPENDENCY_VERSION=$(grep -m 1 "$LIBRARY" pom.xml | cut -d ">" -f 2 | cut -d "<" -f 1) - toggle_version "$BRANCH_NAME" - update_dependency "$DEPENDENCY_REPO" "$NEW_VERSION" "$BRANCH_NAME" - mvn versions:set-property -Dproperty=java-common-libs.version -DnewVersion="$NEW_VERSION" -DgenerateBackupPoms=false - git commit -am "Update '$LIBRARY' dependency to $NEW_VERSION" -} - - -if [ "$LIB" = "JAVA_COMMONS_LIB" ];then - update_library java-common-libs.version -fi -if [ "$LIB" = "BIODATA" ];then - update_library biodata.version -fi - -yellow "The new dependency version is $NEW_VERSION" -cd "$CURRENT_DIR" || exit 2 From 691f36abdca237a3a55ef5e3f84136907eacaa13 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 8 May 2023 18:17:38 +0200 Subject: [PATCH 028/109] cicd: Comment added #TASK-4163 --- .github/workflows/task.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/task.yml b/.github/workflows/task.yml index ae8d4cc8bd1..52394fd2fd5 100644 --- a/.github/workflows/task.yml +++ b/.github/workflows/task.yml @@ -5,7 +5,7 @@ on: branches: - TASK-* workflow_dispatch: - +#WARNING Develop branch needed for prod jobs: build: uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@TASK-4163 From 618603f65a2db073446611025d25071bb4c275c7 Mon Sep 17 00:00:00 2001 From: pfurio Date: Wed, 10 May 2023 15:15:10 +0200 Subject: [PATCH 029/109] catalog: add new method to update user to synced groups, #TASK-4359 --- .../catalog/db/api/StudyDBAdaptor.java | 24 ++- .../mongodb/AuthorizationMongoDBAdaptor.java | 4 +- .../db/mongodb/StudyMongoDBAdaptor.java | 169 +++++++++++++----- .../catalog/managers/AdminManager.java | 96 +++++++++- .../db/mongodb/StudyMongoDBAdaptorTest.java | 73 +++++++- .../core/models/admin/UserUpdateGroup.java | 43 +++++ .../server/rest/admin/AdminWSServer.java | 21 ++- 7 files changed, 382 insertions(+), 48 deletions(-) create mode 100644 opencga-core/src/main/java/org/opencb/opencga/core/models/admin/UserUpdateGroup.java diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/StudyDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/StudyDBAdaptor.java index 65077320bb7..f74d1a843b7 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/StudyDBAdaptor.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/StudyDBAdaptor.java @@ -25,6 +25,7 @@ import org.opencb.opencga.catalog.exceptions.CatalogAuthorizationException; import org.opencb.opencga.catalog.exceptions.CatalogDBException; import org.opencb.opencga.catalog.exceptions.CatalogParameterException; +import org.opencb.opencga.catalog.utils.ParamUtils; import org.opencb.opencga.core.models.common.Enums; import org.opencb.opencga.core.models.project.Project; import org.opencb.opencga.core.models.study.*; @@ -287,9 +288,28 @@ OpenCGAResult removeUsersFromAllGroups(long studyId, List users) * @param groupList List containing possible groups that are synced and where the user should be added to. * @param authOrigin Authentication origin of the synced groups. * @return OpenCGAResult object. - * @throws CatalogDBException CatalogDBException. + * @throws CatalogDBException CatalogDBException + * @throws CatalogParameterException CatalogParameterException + * @throws CatalogAuthorizationException CatalogAuthorizationException */ - OpenCGAResult resyncUserWithSyncedGroups(String user, List groupList, String authOrigin) throws CatalogDBException; + OpenCGAResult resyncUserWithSyncedGroups(String user, List groupList, String authOrigin) + throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException; + + /** + * ADD or REMOVE user to list of provided groups. + * + * @param user User id. + * @param studyUids List of study uids. + * @param groupList List of group ids. + * @param action Update action [ADD, REMOVE] + * @return OpenCGAResult object. + * @throws CatalogDBException CatalogDBException + * @throws CatalogParameterException CatalogParameterException + * @throws CatalogAuthorizationException CatalogAuthorizationException + */ + OpenCGAResult updateUserFromGroups(String user, List studyUids, List groupList, + ParamUtils.AddRemoveAction action) + throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException; /** * Create the permission rule to the list of permission rules defined for the entry in the studyId. diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/AuthorizationMongoDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/AuthorizationMongoDBAdaptor.java index edab86e2f36..fff9a1ed3b3 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/AuthorizationMongoDBAdaptor.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/AuthorizationMongoDBAdaptor.java @@ -522,8 +522,8 @@ private void addToMembersGroupInStudy(long studyId, List members, Client .collect(Collectors.toList()); if (CollectionUtils.isNotEmpty(userList)) { // We first add the member to the @members group in case they didn't belong already - dbAdaptorFactory.getCatalogStudyDBAdaptor().addUsersToGroup(studyId, CatalogAuthorizationManager.MEMBERS_GROUP, - userList, clientSession); + dbAdaptorFactory.getCatalogStudyDBAdaptor().addUsersToGroup(clientSession, studyId, CatalogAuthorizationManager.MEMBERS_GROUP, + userList); } } diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/StudyMongoDBAdaptor.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/StudyMongoDBAdaptor.java index 0a3539870bb..34510e96868 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/StudyMongoDBAdaptor.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/mongodb/StudyMongoDBAdaptor.java @@ -29,7 +29,6 @@ import org.opencb.commons.datastore.core.*; import org.opencb.commons.datastore.mongodb.MongoDBCollection; import org.opencb.commons.datastore.mongodb.MongoDBIterator; -import org.opencb.commons.utils.ListUtils; import org.opencb.opencga.catalog.db.api.*; import org.opencb.opencga.catalog.db.mongodb.converters.StudyConverter; import org.opencb.opencga.catalog.db.mongodb.converters.VariableSetConverter; @@ -40,6 +39,7 @@ import org.opencb.opencga.catalog.utils.Constants; import org.opencb.opencga.catalog.utils.ParamUtils; import org.opencb.opencga.catalog.utils.UuidUtils; +import org.opencb.opencga.core.api.ParamConstants; import org.opencb.opencga.core.common.TimeUtils; import org.opencb.opencga.core.config.Configuration; import org.opencb.opencga.core.models.cohort.Cohort; @@ -482,8 +482,8 @@ public OpenCGAResult setUsersToGroup(long studyId, String groupId, List(result); } - void addUsersToGroup(long studyId, String groupId, List members, ClientSession clientSession) throws CatalogDBException { - if (ListUtils.isEmpty(members)) { + void addUsersToGroup(ClientSession clientSession, long studyId, String groupId, List members) throws CatalogDBException { + if (CollectionUtils.isEmpty(members)) { return; } @@ -491,7 +491,7 @@ void addUsersToGroup(long studyId, String groupId, List members, ClientS .append(PRIVATE_UID, studyId) .append(QueryParams.GROUP_ID.key(), groupId); Document update = new Document("$addToSet", new Document("groups.$.userIds", new Document("$each", members))); - DataResult result = studyCollection.update(clientSession, query, update, null); + DataResult result = studyCollection.update(clientSession, query, update, null); if (result.getNumMatches() != 1) { throw new CatalogDBException("Unable to add members to group " + groupId + ". The group does not exist."); @@ -500,7 +500,7 @@ void addUsersToGroup(long studyId, String groupId, List members, ClientS @Override public OpenCGAResult addUsersToGroup(long studyId, String groupId, List members) throws CatalogDBException { - if (ListUtils.isEmpty(members)) { + if (CollectionUtils.isEmpty(members)) { throw new CatalogDBException("List of 'members' is missing or empty."); } @@ -589,56 +589,145 @@ public OpenCGAResult syncGroup(long studyId, String groupId, Group.Sync s return new OpenCGAResult<>(studyCollection.update(query, updates, null)); } - // TODO: Make this transactional @Override public OpenCGAResult resyncUserWithSyncedGroups(String user, List groupList, String authOrigin) - throws CatalogDBException { + throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException { if (StringUtils.isEmpty(user)) { throw new CatalogDBException("Missing user field"); } - // 1. Take the user out from all synced groups - Document query = new Document() - .append(QueryParams.GROUPS.key(), new Document("$elemMatch", new Document() - .append("userIds", user) - .append("syncedFrom.authOrigin", authOrigin) - )); - Bson pull = Updates.pull("groups.$.userIds", user); - - // Pull the user while it still belongs to a synced group - QueryOptions multi = new QueryOptions(MongoDBCollection.MULTI, true); - DataResult update; - do { - update = studyCollection.update(query, pull, multi); - } while (update.getNumUpdated() > 0); - - // 2. Add user to all synced groups - if (groupList != null && groupList.size() > 0) { - // Add the user to all the synced groups matching - query = new Document() + return runTransaction(clientSession -> { + // 1. Take the user out from all synced groups + Document query = new Document() .append(QueryParams.GROUPS.key(), new Document("$elemMatch", new Document() - .append("userIds", new Document("$ne", user)) - .append("syncedFrom.remoteGroup", new Document("$in", groupList)) + .append("userIds", user) .append("syncedFrom.authOrigin", authOrigin) )); - Document push = new Document("$addToSet", new Document("groups.$.userIds", user)); + Bson pull = Updates.pull("groups.$.userIds", user); + + // Pull the user while it still belongs to a synced group + QueryOptions multi = new QueryOptions(MongoDBCollection.MULTI, true); + DataResult update; do { - update = studyCollection.update(query, push, multi); + update = studyCollection.update(clientSession, query, pull, multi); } while (update.getNumUpdated() > 0); - // We need to be updated with the internal @members group, so we fetch all the studies where the user has been added - // and attempt to add it to the each @members group - query = new Document() - .append(QueryParams.GROUP_USER_IDS.key(), user) - .append(QueryParams.GROUP_SYNCED_FROM_AUTH_ORIGIN.key(), authOrigin); - DataResult studyDataResult = studyCollection.find(query, studyConverter, new QueryOptions(QueryOptions.INCLUDE, - QueryParams.UID.key())); - for (Study study : studyDataResult.getResults()) { - addUsersToGroup(study.getUid(), "@members", Arrays.asList(user)); + // 2. Add user to all synced groups + if (groupList != null && groupList.size() > 0) { + // Add the user to all the synced groups matching + query = new Document() + .append(QueryParams.GROUPS.key(), new Document("$elemMatch", new Document() + .append("userIds", new Document("$ne", user)) + .append("syncedFrom.remoteGroup", new Document("$in", groupList)) + .append("syncedFrom.authOrigin", authOrigin) + )); + Document push = new Document("$addToSet", new Document("groups.$.userIds", user)); + do { + update = studyCollection.update(clientSession, query, push, multi); + } while (update.getNumUpdated() > 0); + + // We need to be updated with the internal @members group, so we fetch all the studies where the user has been added + // and attempt to add it to all @members groups + query = new Document() + .append(QueryParams.GROUP_USER_IDS.key(), user) + .append(QueryParams.GROUP_SYNCED_FROM_AUTH_ORIGIN.key(), authOrigin); + DataResult studyDataResult = studyCollection.find(clientSession, query, studyConverter, + new QueryOptions(QueryOptions.INCLUDE, QueryParams.UID.key())); + for (Study study : studyDataResult.getResults()) { + addUsersToGroup(clientSession, study.getUid(), "@members", Collections.singletonList(user)); + } } + + return OpenCGAResult.empty(Group.class); + }); + } + + @Override + public OpenCGAResult updateUserFromGroups(String user, List studyUids, List groupList, + ParamUtils.AddRemoveAction action) + throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException { + + if (StringUtils.isEmpty(user)) { + throw new CatalogParameterException("Missing user parameter"); + } + if (action == null) { + throw new CatalogParameterException("Missing action parameter"); + } + if (CollectionUtils.isEmpty(groupList)) { + throw new CatalogParameterException("Missing list of groups"); } - return OpenCGAResult.empty(); + // Fix group ids + List fixedGroupList = groupList.stream() + .map((group) -> { + if (!group.startsWith("@")) { + return "@" + group; + } + return group; + }) + .collect(Collectors.toList()); + + QueryOptions multi = new QueryOptions(MongoDBCollection.MULTI, true); + + return runTransaction(clientSession -> { + switch (action) { + case ADD: + Document addQuery = new Document() + // Do not apply changes in the admin study + .append(QueryParams.FQN.key(), new Document("$ne", ParamConstants.ADMIN_STUDY_FQN)) + // Add the user to all the groups matching the list + .append(QueryParams.GROUPS.key(), new Document("$elemMatch", new Document() + .append("userIds", new Document("$ne", user)) + .append("id", new Document("$in", fixedGroupList)) + )); + if (studyUids != null) { + addQuery.put(QueryParams.UID.key(), new Document("$in", studyUids)); + } + + Document push = new Document("$addToSet", new Document("groups.$.userIds", user)); + DataResult update; + do { + update = studyCollection.update(clientSession, addQuery, push, multi); + } while (update.getNumUpdated() > 0); + + // We need to be updated with the internal @members group, so we fetch all the studies where the user has been added + // and attempt to add it to all @members groups + addQuery = new Document() + .append(QueryParams.GROUP_USER_IDS.key(), user) + .append(QueryParams.GROUP_ID.key(), new Document("$in", fixedGroupList)); + if (studyUids != null) { + addQuery.put(QueryParams.UID.key(), new Document("$in", studyUids)); + } + + DataResult studyDataResult = studyCollection.find(clientSession, addQuery, studyConverter, + new QueryOptions(QueryOptions.INCLUDE, QueryParams.UID.key())); + for (Study study : studyDataResult.getResults()) { + addUsersToGroup(clientSession, study.getUid(), "@members", Collections.singletonList(user)); + } + break; + case REMOVE: + // 1. Take the user out from all groups + Document removeQuery = new Document() + .append(QueryParams.GROUPS.key(), new Document("$elemMatch", new Document() + .append("userIds", user) + .append("id", new Document("$in", fixedGroupList)) + )); + if (studyUids != null) { + removeQuery.put(QueryParams.UID.key(), new Document("$in", studyUids)); + } + Bson pull = Updates.pull("groups.$.userIds", user); + DataResult pullUpdate; + do { + pullUpdate = studyCollection.update(clientSession, removeQuery, pull, multi); + } while (pullUpdate.getNumUpdated() > 0); + + break; + default: + break; + } + + return OpenCGAResult.empty(Group.class); + }); } @Override diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/AdminManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/AdminManager.java index 3bffa773511..69e1b0f14dc 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/AdminManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/AdminManager.java @@ -3,7 +3,6 @@ import org.opencb.commons.datastore.core.ObjectMap; import org.opencb.commons.datastore.core.Query; import org.opencb.commons.datastore.core.QueryOptions; -import org.opencb.opencga.core.models.audit.AuditRecord; import org.opencb.opencga.catalog.auth.authorization.AuthorizationManager; import org.opencb.opencga.catalog.db.DBAdaptorFactory; import org.opencb.opencga.catalog.db.api.UserDBAdaptor; @@ -12,12 +11,18 @@ import org.opencb.opencga.catalog.utils.ParamUtils; import org.opencb.opencga.core.api.ParamConstants; import org.opencb.opencga.core.config.Configuration; +import org.opencb.opencga.core.models.audit.AuditRecord; import org.opencb.opencga.core.models.common.Enums; +import org.opencb.opencga.core.models.study.Group; +import org.opencb.opencga.core.models.study.Study; import org.opencb.opencga.core.models.user.User; import org.opencb.opencga.core.response.OpenCGAResult; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import java.util.ArrayList; +import java.util.List; + public class AdminManager extends AbstractManager { private final CatalogIOManager catalogIOManager; @@ -72,4 +77,93 @@ public OpenCGAResult userSearch(Query query, QueryOptions options, String } } + public OpenCGAResult updateGroups(String userId, List studyIds, List groupIds, + ParamUtils.AddRemoveAction action, String token) throws CatalogException { + ObjectMap auditParams = new ObjectMap() + .append("userId", userId) + .append("studyIds", studyIds) + .append("groupIds", groupIds) + .append("action", action) + .append("token", token); + String authenticatedUser = catalogManager.getUserManager().getUserId(token); + try { + authorizationManager.checkIsInstallationAdministrator(authenticatedUser); + + // Check userId exists + Query query = new Query(UserDBAdaptor.QueryParams.ID.key(), userId); + OpenCGAResult count = userDBAdaptor.count(query); + if (count.getNumMatches() == 0) { + throw new CatalogException("User '" + userId + "' not found."); + } + + boolean membersPassed = groupIds.stream().anyMatch(g -> g.startsWith("@") + ? ParamConstants.MEMBERS_GROUP.equals(g) + : ParamConstants.MEMBERS_GROUP.equals("@" + g)); + if (action.equals(ParamUtils.AddRemoveAction.REMOVE) && membersPassed) { + // TODO: If @members is added for REMOVAL, we should also automatically remove all permissions. + throw new CatalogException("Operation not supported for '@members' group."); + } + + // Check studyIds exist + List studies = catalogManager.getStudyManager().resolveIds(studyIds, authenticatedUser); + List studyUids = new ArrayList<>(studies.size()); + for (Study study : studies) { + if (ParamConstants.ADMIN_STUDY_FQN.equals(study.getFqn())) { + throw new CatalogException("Cannot perform this operation on administration study '" + study.getFqn() + "'."); + } + studyUids.add(study.getUid()); + } + + OpenCGAResult result = studyDBAdaptor.updateUserFromGroups(userId, studyUids, groupIds, action); + + auditManager.audit(userId, Enums.Action.UPDATE_USERS_FROM_STUDY_GROUP, Enums.Resource.STUDY, "", "", "", "", auditParams, + new AuditRecord.Status(AuditRecord.Status.Result.SUCCESS)); + return result; + } catch (CatalogException e) { + auditManager.audit(userId, Enums.Action.UPDATE_USERS_FROM_STUDY_GROUP, Enums.Resource.STUDY, "", "", "", "", auditParams, + new AuditRecord.Status(AuditRecord.Status.Result.ERROR, e.getError())); + throw e; + } + } + + /** + * Add a user to all the remote groups he/she may belong for a particular authentication origin. + * Also remove the user from other groups he/she may have been associated in the past for the same authentication origin. + * + * @param userId User id. + * @param remoteGroupIds List of group ids the user must be associated with. + * @param authenticationOriginId The authentication origin the groups must be associated to. + * @param token Administrator token. + * @return An empty OpenCGAResult. + * @throws CatalogException If the token is invalid or belongs to a user other thant the Administrator and if userId does not exist. + */ + public OpenCGAResult syncRemoteGroups(String userId, List remoteGroupIds, + String authenticationOriginId, String token) throws CatalogException { + ObjectMap auditParams = new ObjectMap() + .append("userId", userId) + .append("remoteGroupIds", remoteGroupIds) + .append("authenticationOriginId", authenticationOriginId) + .append("token", token); + String authenticatedUser = catalogManager.getUserManager().getUserId(token); + try { + authorizationManager.checkIsInstallationAdministrator(authenticatedUser); + + // Check userId exists + Query query = new Query(UserDBAdaptor.QueryParams.ID.key(), userId); + OpenCGAResult count = userDBAdaptor.count(query); + if (count.getNumMatches() == 0) { + throw new CatalogException("User '" + userId + "' not found."); + } + OpenCGAResult result = studyDBAdaptor.resyncUserWithSyncedGroups(userId, remoteGroupIds, authenticationOriginId); + + auditManager.audit(userId, Enums.Action.UPDATE_USERS_FROM_STUDY_GROUP, Enums.Resource.STUDY, "", "", "", "", auditParams, + new AuditRecord.Status(AuditRecord.Status.Result.SUCCESS)); + return result; + } catch (CatalogException e) { + auditManager.audit(userId, Enums.Action.UPDATE_USERS_FROM_STUDY_GROUP, Enums.Resource.STUDY, "", "", "", "", auditParams, + new AuditRecord.Status(AuditRecord.Status.Result.ERROR, e.getError())); + throw e; + } + } + } diff --git a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/db/mongodb/StudyMongoDBAdaptorTest.java b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/db/mongodb/StudyMongoDBAdaptorTest.java index f8c7b20e550..5791005394c 100644 --- a/opencga-catalog/src/test/java/org/opencb/opencga/catalog/db/mongodb/StudyMongoDBAdaptorTest.java +++ b/opencga-catalog/src/test/java/org/opencb/opencga/catalog/db/mongodb/StudyMongoDBAdaptorTest.java @@ -26,6 +26,7 @@ import org.opencb.opencga.catalog.exceptions.CatalogDBException; import org.opencb.opencga.catalog.exceptions.CatalogException; import org.opencb.opencga.catalog.exceptions.CatalogParameterException; +import org.opencb.opencga.catalog.utils.ParamUtils; import org.opencb.opencga.core.models.study.*; import org.opencb.opencga.core.testclassification.duration.MediumTests; @@ -208,7 +209,7 @@ public void removeUsersFromAllGroups() throws CatalogDBException, CatalogParamet } @Test - public void resyncUserWithSyncedGroups() throws CatalogDBException { + public void resyncUserWithSyncedGroups() throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException { // We create synced groups and not synced groups in study 5 Group group = new Group("@notSyncedGroup", Arrays.asList("user1", "user2", "user3")); catalogStudyDBAdaptor.createGroup(5L, group); @@ -275,4 +276,74 @@ public void resyncUserWithSyncedGroups() throws CatalogDBException { .containsAll(Arrays.asList("@notSyncedGroup", "@syncedGroup2", "@syncedGroup3", "@members"))); } + @Test + public void updateUserToGroups() throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException { + // We create synced groups and not synced groups in study 5 + Group group = new Group("@notSyncedGroup", Collections.emptyList()); + catalogStudyDBAdaptor.createGroup(5L, group); + group.setId("@syncedGroup1"); + group.setSyncedFrom(new Group.Sync("origin1", "@syncedGroup1")); + catalogStudyDBAdaptor.createGroup(5L, group); + group.setId("@syncedGroup2"); + group.setSyncedFrom(new Group.Sync("origin1", "@syncedGroup2")); + catalogStudyDBAdaptor.createGroup(5L, group); + group.setId("@syncedGroup3"); + group.setSyncedFrom(new Group.Sync("otherOrigin", "@syncedGroup3")); + catalogStudyDBAdaptor.createGroup(5L, group); + + // We create the same synced groups and not synced groups in study 9 + group = new Group("@notSyncedGroup", Collections.emptyList()); + catalogStudyDBAdaptor.createGroup(9L, group); + group.setId("@syncedGroup1"); + group.setSyncedFrom(new Group.Sync("origin1", "@syncedGroup1")); + catalogStudyDBAdaptor.createGroup(9L, group); + group.setId("@syncedGroup2"); + group.setSyncedFrom(new Group.Sync("origin1", "@syncedGroup2")); + catalogStudyDBAdaptor.createGroup(9L, group); + group.setId("@syncedGroup3"); + group.setSyncedFrom(new Group.Sync("otherOrigin", "@syncedGroup3")); + catalogStudyDBAdaptor.createGroup(9L, group); + group = new Group("@otherNotSyncedGroup", Collections.emptyList()); + catalogStudyDBAdaptor.createGroup(9L, group); + + catalogStudyDBAdaptor.updateUserFromGroups("user2", null, Arrays.asList("syncedGroup1", "notSyncedGroup"), ParamUtils.AddRemoveAction.ADD); + DataResult groupsStudy1 = catalogStudyDBAdaptor.getGroup(5L, null, Arrays.asList("user2")); + DataResult groupsStudy2 = catalogStudyDBAdaptor.getGroup(9L, null, Arrays.asList("user2")); + assertEquals(groupsStudy1.getNumResults(), groupsStudy2.getNumResults()); + assertEquals(3, groupsStudy1.getNumResults()); + assertTrue(groupsStudy1.getResults().stream().map(Group::getId).collect(Collectors.toList()) + .containsAll(Arrays.asList("@notSyncedGroup", "@syncedGroup1", "@members"))); + assertEquals(3, groupsStudy2.getNumResults()); + assertTrue(groupsStudy2.getResults().stream().map(Group::getId).collect(Collectors.toList()) + .containsAll(Arrays.asList("@notSyncedGroup", "@syncedGroup1", "@members"))); + + catalogStudyDBAdaptor.updateUserFromGroups("user2", null, Arrays.asList("syncedGroup1", "notSyncedGroup"), ParamUtils.AddRemoveAction.REMOVE); + groupsStudy1 = catalogStudyDBAdaptor.getGroup(5L, null, Arrays.asList("user2")); + groupsStudy2 = catalogStudyDBAdaptor.getGroup(9L, null, Arrays.asList("user2")); + assertEquals(1, groupsStudy1.getNumResults()); + assertEquals(1, groupsStudy2.getNumResults()); + assertEquals("@members", groupsStudy1.first().getId()); + assertEquals("@members", groupsStudy2.first().getId()); + + catalogStudyDBAdaptor.updateUserFromGroups("user2", Arrays.asList(5L, 9L), Arrays.asList("syncedGroup1", "notSyncedGroup"), ParamUtils.AddRemoveAction.ADD); + groupsStudy1 = catalogStudyDBAdaptor.getGroup(5L, null, Arrays.asList("user2")); + groupsStudy2 = catalogStudyDBAdaptor.getGroup(9L, null, Arrays.asList("user2")); + assertEquals(groupsStudy1.getNumResults(), groupsStudy2.getNumResults()); + assertEquals(3, groupsStudy1.getNumResults()); + assertTrue(groupsStudy1.getResults().stream().map(Group::getId).collect(Collectors.toList()) + .containsAll(Arrays.asList("@notSyncedGroup", "@syncedGroup1", "@members"))); + assertEquals(3, groupsStudy2.getNumResults()); + assertTrue(groupsStudy2.getResults().stream().map(Group::getId).collect(Collectors.toList()) + .containsAll(Arrays.asList("@notSyncedGroup", "@syncedGroup1", "@members"))); + + catalogStudyDBAdaptor.updateUserFromGroups("user2", Collections.singletonList(5L), Arrays.asList("syncedGroup1", "notSyncedGroup"), ParamUtils.AddRemoveAction.REMOVE); + groupsStudy1 = catalogStudyDBAdaptor.getGroup(5L, null, Arrays.asList("user2")); + groupsStudy2 = catalogStudyDBAdaptor.getGroup(9L, null, Arrays.asList("user2")); + assertEquals(1, groupsStudy1.getNumResults()); + assertEquals("@members", groupsStudy1.first().getId()); + assertEquals(3, groupsStudy2.getNumResults()); + assertTrue(groupsStudy2.getResults().stream().map(Group::getId).collect(Collectors.toList()) + .containsAll(Arrays.asList("@notSyncedGroup", "@syncedGroup1", "@members"))); + } + } diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/admin/UserUpdateGroup.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/admin/UserUpdateGroup.java new file mode 100644 index 00000000000..ce05d03ccc2 --- /dev/null +++ b/opencga-core/src/main/java/org/opencb/opencga/core/models/admin/UserUpdateGroup.java @@ -0,0 +1,43 @@ +package org.opencb.opencga.core.models.admin; + +import java.util.List; + +public class UserUpdateGroup { + private List studyIds; + private List groupIds; + + public UserUpdateGroup() { + } + + public UserUpdateGroup(List studyIds, List groupIds) { + this.studyIds = studyIds; + this.groupIds = groupIds; + } + + @Override + public String toString() { + final StringBuilder sb = new StringBuilder("UserUpdateGroup{"); + sb.append("studyIds=").append(studyIds); + sb.append(", groupIds=").append(groupIds); + sb.append('}'); + return sb.toString(); + } + + public List getStudyIds() { + return studyIds; + } + + public UserUpdateGroup setStudyIds(List studyIds) { + this.studyIds = studyIds; + return this; + } + + public List getGroupIds() { + return groupIds; + } + + public UserUpdateGroup setGroupIds(List groupIds) { + this.groupIds = groupIds; + return this; + } +} diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/rest/admin/AdminWSServer.java b/opencga-server/src/main/java/org/opencb/opencga/server/rest/admin/AdminWSServer.java index f07c7ad3ecb..835c9632af1 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/rest/admin/AdminWSServer.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/rest/admin/AdminWSServer.java @@ -16,8 +16,6 @@ package org.opencb.opencga.server.rest.admin; -import org.opencb.opencga.core.models.user.AuthenticationResponse; -import org.opencb.opencga.core.tools.annotations.*; import org.apache.commons.lang3.StringUtils; import org.opencb.commons.datastore.core.DataResult; import org.opencb.commons.datastore.core.ObjectMap; @@ -31,6 +29,7 @@ import org.opencb.opencga.analysis.sample.SampleIndexTask; import org.opencb.opencga.catalog.db.api.MetaDBAdaptor; import org.opencb.opencga.catalog.exceptions.CatalogException; +import org.opencb.opencga.catalog.utils.ParamUtils; import org.opencb.opencga.core.api.ParamConstants; import org.opencb.opencga.core.exceptions.VersionException; import org.opencb.opencga.core.models.admin.*; @@ -39,8 +38,10 @@ import org.opencb.opencga.core.models.sample.Sample; import org.opencb.opencga.core.models.study.Group; import org.opencb.opencga.core.models.user.Account; +import org.opencb.opencga.core.models.user.AuthenticationResponse; import org.opencb.opencga.core.models.user.User; import org.opencb.opencga.core.response.OpenCGAResult; +import org.opencb.opencga.core.tools.annotations.*; import org.opencb.opencga.server.rest.OpenCGAWSServer; import javax.servlet.http.HttpServletRequest; @@ -153,6 +154,22 @@ public Response remoteImport(@ApiParam(value = "JSON containing the parameters", } } + @POST + @Path("/users/{user}/groups/update") + @Consumes(MediaType.APPLICATION_JSON) + @ApiOperation(value = "Add or remove users from existing groups", response = Group.class) + public Response updateGroups( + @ApiParam(value = ParamConstants.USER_DESCRIPTION) @PathParam(ParamConstants.USER) String user, + @ApiParam(value = "Action to be performed: ADD or REMOVE user to/from groups", allowableValues = "ADD,REMOVE", + defaultValue = "ADD") @QueryParam("action") ParamUtils.AddRemoveAction action, + @ApiParam(value = "JSON containing the parameters", required = true) UserUpdateGroup updateParams) { + try { + return createOkResponse(catalogManager.getAdminManager().updateGroups(user, updateParams.getStudyIds(), updateParams.getGroupIds(), action, token)); + } catch (Exception e) { + return createErrorResponse(e); + } + } + @POST @Path("/users/sync") @ApiOperation(value = "Synchronise a group of users from an authentication origin with a group in a study from catalog", response = Group.class, From 1340a9b4b8949a883cb8d91a4665fe768c8248d7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Fri, 12 May 2023 09:38:08 +0100 Subject: [PATCH 030/109] docker: Add yq to opencga-base. #TASK-4192 --- opencga-app/app/cloud/docker/opencga-base/Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/opencga-app/app/cloud/docker/opencga-base/Dockerfile b/opencga-app/app/cloud/docker/opencga-base/Dockerfile index 3d2c1e4db7c..5132720657c 100644 --- a/opencga-app/app/cloud/docker/opencga-base/Dockerfile +++ b/opencga-app/app/cloud/docker/opencga-base/Dockerfile @@ -16,6 +16,8 @@ RUN apt-get update && apt-get -y upgrade && apt-get install -y lsb-release sshpa echo "deb http://repo.mongodb.org/apt/debian buster/mongodb-org/4.2 main" | tee /etc/apt/sources.list.d/mongodb-org-4.2.list && \ apt-get update && apt-get install -y docker-ce docker-ce-cli containerd.io mongodb-org-shell && \ rm -rf /var/lib/apt/lists/* && \ + wget -qO /usr/local/bin/yq https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64 && \ + chmod +x /usr/local/bin/yq && \ adduser --disabled-password --uid 1001 opencga ## Run Docker images as non root From 1cbf0f66177f4116348be5294e2021da39078ca1 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 12 May 2023 18:24:54 +0200 Subject: [PATCH 031/109] Port Patch v1.6.1 #TASK-4371 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-deps-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp2.6/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 2 +- 21 files changed, 21 insertions(+), 21 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 9c2c2562870..10184c4d1ae 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.1 + 2.9.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 79682c8727f..4ac72115c89 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.1 + 2.9.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index c9cc7490a76..1bded6a828a 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 2.8.1 + 2.9.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 616d1d68e08..cc666ed2646 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.1 + 2.9.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index e831de167b0..88157b769f9 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 2.8.1 + 2.9.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index b677e8ff1dc..f8a759696b8 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.1 + 2.9.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 39f2be6312e..6bcfe1229a1 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 2.8.1 + 2.9.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index b873573e930..146bfdcb0f1 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.1 + 2.9.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index a6ee7b85941..762d12d1730 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.8.1 + 2.9.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 372b65863eb..611100fea78 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 2.8.1 + 2.9.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index bf4fdf2917e..830a04cf6c9 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -25,7 +25,7 @@ org.opencb.opencga opencga-storage - 2.8.1 + 2.9.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 6c2f0b54bd5..8aefe17d973 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.8.1 + 2.9.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml index 2157ccc69e5..5da87ce97ea 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.8.1 + 2.9.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml index b4685ef3354..938346bf05a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.8.1 + 2.9.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml index 0e6ff804ca8..606c47dea2b 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.8.1 + 2.9.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml index 627dc2bdd3c..320691d8782 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml @@ -50,7 +50,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.8.1 + 2.9.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 20b6e62754f..da7ae969c7d 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -28,7 +28,7 @@ org.opencb.opencga opencga-storage - 2.8.1 + 2.9.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index aba64ebc3b7..4a66ba429de 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.8.1 + 2.9.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index c606422a941..8276f52ef48 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.1 + 2.9.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 402cefdbd2e..08a12d4c1e6 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 2.8.1 + 2.9.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index fc1a5f52f8b..db0b212b7ee 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.1 + 2.9.0-SNAPSHOT pom OpenCGA OenCGA projects implements a big data platform for genomic data analysis From 3d948d83c56b88ab56ec9126e2f4030c14033055 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 15 May 2023 11:27:37 +0200 Subject: [PATCH 032/109] cicd: References to develop updated #TASK-4163 --- .github/workflows/task.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/task.yml b/.github/workflows/task.yml index 52394fd2fd5..a73d0c10c64 100644 --- a/.github/workflows/task.yml +++ b/.github/workflows/task.yml @@ -8,7 +8,7 @@ on: #WARNING Develop branch needed for prod jobs: build: - uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@TASK-4163 + uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop with: maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' From 283042643c6574bcb1441361beb3b00d195a4754 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Mon, 15 May 2023 18:47:20 +0100 Subject: [PATCH 033/109] storage: Use default datarelease by version instead of "latest". #TASK-4332 --- .../core/cellbase/CellBaseValidator.java | 50 +++++++++++++++---- .../storage/core/utils/CellBaseUtilsTest.java | 3 +- pom.xml | 2 +- 3 files changed, 42 insertions(+), 13 deletions(-) diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java b/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java index a2c5da2dc72..67cddd88ef1 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java @@ -17,7 +17,7 @@ import java.util.ArrayList; import java.util.Comparator; import java.util.List; -import java.util.Optional; +import java.util.stream.Collectors; public class CellBaseValidator { @@ -94,17 +94,33 @@ public CellBaseConfiguration getCellBaseConfiguration() { return new CellBaseConfiguration(getURL(), getVersion(), getDataRelease(), getToken()); } - public String getLatestActiveDataRelease() throws IOException { + public String getDefaultDataRelease() throws IOException { if (supportsDataRelease()) { - Optional dataRelease = cellBaseClient.getMetaClient().dataReleases() - .allResults() - .stream() - .filter(DataRelease::isActive) - .max(Comparator.comparing(DataRelease::getDate)); - if (!dataRelease.isPresent()) { + List dataReleases = cellBaseClient.getMetaClient().dataReleases() + .allResults(); + DataRelease dataRelease = null; + if (supportsDataReleaseActiveByDefaultIn()) { + // ActiveByDefault versions are stored in form `v.` , i.e. v5.5 , v5.7, ... + String majorMinor = "v" + getVersionFromServerMajorMinor(); + List drs = dataReleases + .stream() + .filter(dr -> dr.getActiveByDefaultIn() != null && dr.getActiveByDefaultIn().contains(majorMinor)) + .collect(Collectors.toList()); + if (drs.size() == 1) { + dataRelease = drs.get(0); + } else if (drs.size() > 1) { + throw new IllegalArgumentException("More than one default active data releases found on cellbase " + this); + } + } else { + dataRelease = dataReleases + .stream() + .filter(DataRelease::isActive) + .max(Comparator.comparing(DataRelease::getDate)).orElse(null); + } + if (dataRelease == null) { throw new IllegalArgumentException("No active data releases found on cellbase " + this); } else { - return String.valueOf(dataRelease.get().getRelease()); + return String.valueOf(dataRelease.getRelease()); } } else { return null; @@ -149,7 +165,7 @@ public CellBaseConfiguration validate(boolean autoComplete) throws IOException { String dataRelease = getDataRelease(); if (dataRelease == null) { if (autoComplete) { - cellBaseConfiguration.setDataRelease(getLatestActiveDataRelease()); + cellBaseConfiguration.setDataRelease(getDefaultDataRelease()); } else { throw new IllegalArgumentException("Missing DataRelease for cellbase " + "url: '" + getURL() + "'" @@ -202,10 +218,19 @@ public boolean supportsDataRelease() throws IOException { } public static boolean supportsDataRelease(String serverVersion) { - // Data Release support starts at versio 5.1.0 + // Data Release support starts at version 5.1.0 return VersionUtils.isMinVersion("5.1.0", serverVersion); } + public boolean supportsDataReleaseActiveByDefaultIn() throws IOException { + return supportsDataReleaseActiveByDefaultIn(getVersionFromServer()); + } + + public static boolean supportsDataReleaseActiveByDefaultIn(String serverVersion) { + // Data Release Default Active In Version support starts at version 5.5.0 , TASK-4157 + return VersionUtils.isMinVersion("5.5.0", serverVersion); + } + public String getVersionFromServerMajor() throws IOException { return major(getVersionFromServer()); } @@ -217,10 +242,13 @@ public String getVersionFromServerMajorMinor() throws IOException { } private static String major(String version) { +// return String.valueOf(new VersionUtils.Version(version).getMajor()); return version.split("\\.")[0]; } private static String majorMinor(String version) { +// VersionUtils.Version v = new VersionUtils.Version(version); +// return v.getMajor() + "." + v.getMinor(); String[] split = version.split("\\."); if (split.length > 1) { version = split[0] + "." + split[1]; diff --git a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/utils/CellBaseUtilsTest.java b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/utils/CellBaseUtilsTest.java index ccb8106a2c0..1f679ace47e 100644 --- a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/utils/CellBaseUtilsTest.java +++ b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/utils/CellBaseUtilsTest.java @@ -67,7 +67,8 @@ public static List data() { new Object[]{"https://ws.zettagenomics.com/cellbase/", "v5.1", "grch38", "1"}, new Object[]{"https://ws.zettagenomics.com/cellbase/", "v5.1", "grch38", "2"}, new Object[]{"https://uk.ws.zettagenomics.com/cellbase/", "v5.2", "grch37", "1"}, - new Object[]{"https://uk.ws.zettagenomics.com/cellbase/", "v5.2", "grch38", "2"}); + new Object[]{"https://uk.ws.zettagenomics.com/cellbase/", "v5.2", "grch38", "2"}, + new Object[]{"https://uk.ws.zettagenomics.com/cellbase/", "v5.4", "grch38", "3"}); } @Parameter(0) diff --git a/pom.xml b/pom.xml index db0b212b7ee..c65e55ff724 100644 --- a/pom.xml +++ b/pom.xml @@ -44,7 +44,7 @@ 2.8.1 2.8.1 - 5.4.0 + 5.5.0-SNAPSHOT 2.8.0 4.8.0 2.8.1 From 6919928ae410d17038468c0f769ab50126ed4f47 Mon Sep 17 00:00:00 2001 From: pfurio Date: Tue, 16 May 2023 10:24:28 +0200 Subject: [PATCH 034/109] catalog: fail if user is passing administration study, #TASK-4359 --- .../opencb/opencga/catalog/managers/AdminManager.java | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/AdminManager.java b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/AdminManager.java index 69e1b0f14dc..b57426ebf04 100644 --- a/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/AdminManager.java +++ b/opencga-catalog/src/main/java/org/opencb/opencga/catalog/managers/AdminManager.java @@ -1,5 +1,6 @@ package org.opencb.opencga.catalog.managers; +import org.apache.commons.collections4.CollectionUtils; import org.opencb.commons.datastore.core.ObjectMap; import org.opencb.commons.datastore.core.Query; import org.opencb.commons.datastore.core.QueryOptions; @@ -109,9 +110,13 @@ public OpenCGAResult updateGroups(String userId, List studyIds, L List studyUids = new ArrayList<>(studies.size()); for (Study study : studies) { if (ParamConstants.ADMIN_STUDY_FQN.equals(study.getFqn())) { - throw new CatalogException("Cannot perform this operation on administration study '" + study.getFqn() + "'."); + if (CollectionUtils.isNotEmpty(studyIds)) { + // Only fail if the user is passing the list of study ids + throw new CatalogException("Cannot perform this operation on administration study '" + study.getFqn() + "'."); + } + } else { + studyUids.add(study.getUid()); } - studyUids.add(study.getUid()); } OpenCGAResult result = studyDBAdaptor.updateUserFromGroups(userId, studyUids, groupIds, action); From dc8b46b1008eead0fbafb116a90671f7212ee07b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Fri, 19 May 2023 14:40:08 +0100 Subject: [PATCH 035/109] storage: Allow working with pre-release cellbase instances. #TASK-4332 --- .../core/cellbase/CellBaseValidator.java | 2 +- .../opencga/core/common/VersionUtils.java | 20 ++++++++++++++++++- 2 files changed, 20 insertions(+), 2 deletions(-) diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java b/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java index 67cddd88ef1..21f5c79fecd 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java @@ -228,7 +228,7 @@ public boolean supportsDataReleaseActiveByDefaultIn() throws IOException { public static boolean supportsDataReleaseActiveByDefaultIn(String serverVersion) { // Data Release Default Active In Version support starts at version 5.5.0 , TASK-4157 - return VersionUtils.isMinVersion("5.5.0", serverVersion); + return VersionUtils.isMinVersion("5.5.0", serverVersion, true); } public String getVersionFromServerMajor() throws IOException { diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/common/VersionUtils.java b/opencga-core/src/main/java/org/opencb/opencga/core/common/VersionUtils.java index fb70ed94cb9..4e32c6ada32 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/common/VersionUtils.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/common/VersionUtils.java @@ -13,7 +13,11 @@ public static List order(List versions) { } public static boolean isMinVersion(String minVersion, String version) { - return new Version(minVersion).compareTo(new Version(version)) <= 0; + return isMinVersion(minVersion, version, false); + } + + public static boolean isMinVersion(String minVersion, String version, boolean ignorePreReleaseVersioning) { + return new Version(minVersion).compareTo(new Version(version), ignorePreReleaseVersioning) <= 0; } public static class Version implements Comparable { @@ -48,6 +52,12 @@ public static class Version implements Comparable { return o1.other.compareTo(o2.other); }); + public static final Comparator COMPARATOR_NO_PR = Comparator + .comparingInt(Version::getMajor) + .thenComparingInt(Version::getMinor) + .thenComparingInt(Version::getPatch) + .thenComparingInt(Version::getRepatch); + public Version(String version) { String[] split = StringUtils.split(version, ".", 4); major = Integer.parseInt(split[0]); @@ -81,6 +91,14 @@ public int compareTo(Version o) { return COMPARATOR.compare(this, o); } + public int compareTo(Version o, boolean ignorePreReleaseVersioning) { + if (ignorePreReleaseVersioning) { + return COMPARATOR_NO_PR.compare(this, o); + } else { + return COMPARATOR.compare(this, o); + } + } + public int getMajor() { return major; } From 88e668a74603bb1af2c1e52c963cbf66fe8718e2 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 22 May 2023 15:19:13 +0200 Subject: [PATCH 036/109] cicd: New check-junit-test workflow #TASK-4445 --- .github/workflows/check-junit-test.yml | 41 +++++++++++++++++++ .github/workflows/scripts/get_profiles.sh | 30 ++++++++++++++ .github/workflows/test-long-test-analysis.yml | 14 ------- 3 files changed, 71 insertions(+), 14 deletions(-) create mode 100644 .github/workflows/check-junit-test.yml create mode 100755 .github/workflows/scripts/get_profiles.sh delete mode 100644 .github/workflows/test-long-test-analysis.yml diff --git a/.github/workflows/check-junit-test.yml b/.github/workflows/check-junit-test.yml new file mode 100644 index 00000000000..58f71978a27 --- /dev/null +++ b/.github/workflows/check-junit-test.yml @@ -0,0 +1,41 @@ +name: Check junits + +on: + workflow_dispatch: + inputs: + short_tests: + type: boolean + required: false + default: true + medium_tests: + type: boolean + required: false + default: false + long_tests: + type: boolean + required: false + default: false + mvn_opts: + type: string + required: false + default: "" + +jobs: + test: + name: Test JUnit + runs-on: ubuntu-22.04 + steps: + - name: Building string profiles to run + id: get_profiles + run: | + if [ -f "./.github/workflows/scripts/get_profiles.sh" ]; then + chmod +x ./.github/workflows/scripts/get_profiles.sh + echo "profiles=$(./.github/workflows/scripts/get_profiles.sh ${{ inputs.short_tests }} ${{ inputs.medium_tests }} ${{ inputs.long_tests }})" >> $GITHUB_OUTPUT + fi + - name: Building string profiles to run + uses: ./.github/workflows/test-analysis.yml + secrets: inherit + with: + test_profile: ${{ steps.get_profiles.outputs.profiles }} + report_context: development + mvn_opts: ${{ inputs.mvn_opts }} diff --git a/.github/workflows/scripts/get_profiles.sh b/.github/workflows/scripts/get_profiles.sh new file mode 100755 index 00000000000..fc205968984 --- /dev/null +++ b/.github/workflows/scripts/get_profiles.sh @@ -0,0 +1,30 @@ +#!/bin/bash + +if [ $# -eq 0 ]; then + echo "The arguments must be 3" + exit 1 +fi +PROFILE="" + +if [ $1 == "true" ]; then + PROFILE="${PROFILE}runShortTests," +fi +if [ $2 == "true" ]; then + PROFILE="${PROFILE}runMediumTests," +fi +if [ $3 == "true" ]; then + PROFILE="${PROFILE}runLongTests" +fi + +if [[ "${PROFILE}" == *"," ]]; then + PROFILE="${PROFILE%?}" +fi + +if [ -z "${PROFILE}" ]; then + echo "There must be at least one active profile" + exit 1 +fi + +echo "${PROFILE}" +exit 0 + diff --git a/.github/workflows/test-long-test-analysis.yml b/.github/workflows/test-long-test-analysis.yml deleted file mode 100644 index fe516b75a98..00000000000 --- a/.github/workflows/test-long-test-analysis.yml +++ /dev/null @@ -1,14 +0,0 @@ -name: LONG TEST ANALYSIS - -on: - push: - branches: - - TASK-4149 - -jobs: - test: - uses: ./.github/workflows/test-analysis.yml - secrets: inherit - with: - test_profile: runLongTests,runMediumTests,runShortTests - report_context: development From cf84cc91e5573393cb1c65a0b04cdf85cb36e2bb Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 22 May 2023 15:23:33 +0200 Subject: [PATCH 037/109] cicd: Change test-analysis to adapt for test junit #TASK-4445 --- .github/workflows/test-analysis.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index d01fb65bd62..ca38d16c6b3 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -8,6 +8,10 @@ on: report_context: type: string required: true + mvn_opts: + type: string + required: false + default: "" secrets: SONAR_TOKEN: required: true @@ -77,7 +81,7 @@ jobs: mongodb-version: 6.0 mongodb-replica-set: rs-test - name: Run Junit tests - run: mvn -B verify surefire-report:report -P storage-hadoop,hdp3.1,${{ inputs.test_profile }} -Dcheckstyle.skip -Popencga-storage-hadoop-deps -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' + run: mvn -B verify surefire-report:report -P storage-hadoop,hdp3.1,${{ inputs.test_profile }} -Dcheckstyle.skip -Popencga-storage-hadoop-deps -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' ${{ inputs.mvn_opts }} - name: Upload result dir uses: actions/upload-artifact@v3 with: From df8382a362780cc7d96065ede6e869c0feb6f2ef Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 23 May 2023 11:08:34 +0200 Subject: [PATCH 038/109] pom: Fix dependencies versions --- .github/workflows/check-junit-test.yml | 2 +- pom.xml | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/check-junit-test.yml b/.github/workflows/check-junit-test.yml index 58f71978a27..a75e011ebd9 100644 --- a/.github/workflows/check-junit-test.yml +++ b/.github/workflows/check-junit-test.yml @@ -34,8 +34,8 @@ jobs: fi - name: Building string profiles to run uses: ./.github/workflows/test-analysis.yml - secrets: inherit with: test_profile: ${{ steps.get_profiles.outputs.profiles }} report_context: development mvn_opts: ${{ inputs.mvn_opts }} + secrets: inherit diff --git a/pom.xml b/pom.xml index c65e55ff724..437d0956bf5 100644 --- a/pom.xml +++ b/pom.xml @@ -42,12 +42,12 @@ - 2.8.1 - 2.8.1 + 2.9.0-dev + 2.9.0-dev 5.5.0-SNAPSHOT - 2.8.0 - 4.8.0 - 2.8.1 + 2.9.0-SNAPSHOT + 4.9.0-SNAPSHOT + 2.9.0-SNAPSHOT 0.2.0 2.11.4 From ff1510cd48966aa005b3db61ea7ff204c8047d5b Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 23 May 2023 12:01:17 +0200 Subject: [PATCH 039/109] cicd:secrets error #TASK-4445 --- .github/workflows/check-junit-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check-junit-test.yml b/.github/workflows/check-junit-test.yml index a75e011ebd9..79edaad0923 100644 --- a/.github/workflows/check-junit-test.yml +++ b/.github/workflows/check-junit-test.yml @@ -38,4 +38,4 @@ jobs: test_profile: ${{ steps.get_profiles.outputs.profiles }} report_context: development mvn_opts: ${{ inputs.mvn_opts }} - secrets: inherit + secrets: inherit \ No newline at end of file From 86c583fc710b559427549506354ecaff46e61896 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 23 May 2023 12:12:36 +0200 Subject: [PATCH 040/109] cicd:Add needed checkout step #TASK-4445 --- .github/workflows/check-junit-test.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/check-junit-test.yml b/.github/workflows/check-junit-test.yml index 79edaad0923..4c56f2c2702 100644 --- a/.github/workflows/check-junit-test.yml +++ b/.github/workflows/check-junit-test.yml @@ -25,6 +25,9 @@ jobs: name: Test JUnit runs-on: ubuntu-22.04 steps: + - uses: actions/checkout@v3 + with: + fetch-depth: '10' - name: Building string profiles to run id: get_profiles run: | From 7aae0542e9eacd68bf62592376b9f8b67e2019b2 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 23 May 2023 12:28:13 +0200 Subject: [PATCH 041/109] cicd: Refactor in two jobs #TASK-4445 --- .github/workflows/check-junit-test.yml | 22 +++++++++++++--------- .github/workflows/develop.yml | 8 ++++---- .github/workflows/docker-aws-emr.yml | 4 ++-- .github/workflows/docker-tools.yml | 4 ++-- .github/workflows/pull-request-merge.yml | 2 +- .github/workflows/release.yml | 12 ++++++------ 6 files changed, 28 insertions(+), 24 deletions(-) diff --git a/.github/workflows/check-junit-test.yml b/.github/workflows/check-junit-test.yml index 4c56f2c2702..50e52b894f0 100644 --- a/.github/workflows/check-junit-test.yml +++ b/.github/workflows/check-junit-test.yml @@ -21,24 +21,28 @@ on: default: "" jobs: - test: + get_profiles: name: Test JUnit runs-on: ubuntu-22.04 + outputs: + profile: ${{ steps.getter.outputs.profiles }} steps: - uses: actions/checkout@v3 with: fetch-depth: '10' - name: Building string profiles to run - id: get_profiles + id: getter run: | if [ -f "./.github/workflows/scripts/get_profiles.sh" ]; then chmod +x ./.github/workflows/scripts/get_profiles.sh echo "profiles=$(./.github/workflows/scripts/get_profiles.sh ${{ inputs.short_tests }} ${{ inputs.medium_tests }} ${{ inputs.long_tests }})" >> $GITHUB_OUTPUT fi - - name: Building string profiles to run - uses: ./.github/workflows/test-analysis.yml - with: - test_profile: ${{ steps.get_profiles.outputs.profiles }} - report_context: development - mvn_opts: ${{ inputs.mvn_opts }} - secrets: inherit \ No newline at end of file + + test: + needs: get_profiles + uses: ./.github/workflows/test-analysis.yml + with: + test_profile: ${{ needs.get_profiles.outputs.profiles }} + report_context: development + mvn_opts: ${{ inputs.mvn_opts }} + secrets: inherit \ No newline at end of file diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml index a6d37f1e39c..a6b61a44ee2 100644 --- a/.github/workflows/develop.yml +++ b/.github/workflows/develop.yml @@ -9,12 +9,12 @@ on: jobs: build: - uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.8.x + uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop with: maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' deploy-docker-ext-tools: - uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.8.x + uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: build with: cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }} @@ -29,14 +29,14 @@ jobs: report_context: development deploy-maven: - uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@release-4.8.x + uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop needs: test with: maven_opts: -P storage-hadoop,hdp3.1 -Dopencga.war.name=opencga secrets: inherit deploy-docker: - uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.8.x + uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: test with: cli: python3 ./build/cloud/docker/docker-build.py push --images base,init diff --git a/.github/workflows/docker-aws-emr.yml b/.github/workflows/docker-aws-emr.yml index 98157167216..bf1c8571ca8 100644 --- a/.github/workflows/docker-aws-emr.yml +++ b/.github/workflows/docker-aws-emr.yml @@ -8,12 +8,12 @@ on: jobs: build: - uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.8.x + uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop with: maven_opts: -P storage-hadoop,emr6.1 -Dopencga.war.name=opencga deploy-docker: - uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.8.x + uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: build with: cli: python3 ./build/cloud/docker/docker-build.py push --images base,init diff --git a/.github/workflows/docker-tools.yml b/.github/workflows/docker-tools.yml index 32e938c5a2d..6f61637e0e5 100644 --- a/.github/workflows/docker-tools.yml +++ b/.github/workflows/docker-tools.yml @@ -12,12 +12,12 @@ on: jobs: build: - uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.8.x + uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop with: maven_opts: deploy-docker-ext-tools: - uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.8.x + uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: build with: cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }} diff --git a/.github/workflows/pull-request-merge.yml b/.github/workflows/pull-request-merge.yml index ff9fbdc3c1e..4b1c43c682b 100644 --- a/.github/workflows/pull-request-merge.yml +++ b/.github/workflows/pull-request-merge.yml @@ -10,7 +10,7 @@ on: jobs: delete-docker: - uses: opencb/java-common-libs/.github/workflows/delete-docker-hub-workflow.yml@release-4.8.x + uses: opencb/java-common-libs/.github/workflows/delete-docker-hub-workflow.yml@develop with: cli: python3 ./build/cloud/docker/docker-build.py delete --images base --tag ${{ github.head_ref }} secrets: inherit diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index cdad8273a32..5479fc5bb4c 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -8,12 +8,12 @@ on: jobs: build: - uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.8.x + uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop with: maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' deploy-docker-ext-tools: - uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.8.x + uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: build with: cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }} @@ -28,14 +28,14 @@ jobs: report_context: xetabase deploy-maven: - uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@release-4.8.x + uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop needs: test with: maven_opts: -P storage-hadoop,hdp3.1 -Dopencga.war.name=opencga secrets: inherit deploy-docker: - uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.8.x + uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: test with: cli: python3 ./build/cloud/docker/docker-build.py push --images base,init @@ -44,7 +44,7 @@ jobs: deploy-python: - uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@release-4.8.x + uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop needs: test with: cli: ./clients/python/python-build.sh push @@ -52,7 +52,7 @@ jobs: secrets: inherit release: - uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@release-4.8.x + uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop needs: test with: artifact: build-folder From 9e8b180b4196f5e975ae60811877a8f761807b88 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 23 May 2023 12:33:52 +0200 Subject: [PATCH 042/109] cicd: Adding log #TASK-4445 --- .github/workflows/check-junit-test.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/check-junit-test.yml b/.github/workflows/check-junit-test.yml index 50e52b894f0..f4113c35506 100644 --- a/.github/workflows/check-junit-test.yml +++ b/.github/workflows/check-junit-test.yml @@ -38,6 +38,11 @@ jobs: echo "profiles=$(./.github/workflows/scripts/get_profiles.sh ${{ inputs.short_tests }} ${{ inputs.medium_tests }} ${{ inputs.long_tests }})" >> $GITHUB_OUTPUT fi + echo_log: + needs: get_profiles + runs-on: ubuntu-22.04 + run: echo "Executing testing profiles -> ${{ needs.get_profiles.outputs.profiles }}" + test: needs: get_profiles uses: ./.github/workflows/test-analysis.yml From a051044b1ba974b82af65453ad013eb8f9c0ca46 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 23 May 2023 12:36:33 +0200 Subject: [PATCH 043/109] cicd: Adding log #TASK-4445 --- .github/workflows/check-junit-test.yml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/.github/workflows/check-junit-test.yml b/.github/workflows/check-junit-test.yml index f4113c35506..809ce259828 100644 --- a/.github/workflows/check-junit-test.yml +++ b/.github/workflows/check-junit-test.yml @@ -41,10 +41,13 @@ jobs: echo_log: needs: get_profiles runs-on: ubuntu-22.04 - run: echo "Executing testing profiles -> ${{ needs.get_profiles.outputs.profiles }}" + steps: + - name: Echo profiles + id: log + run: echo "Executing testing profiles -> ${{ needs.get_profiles.outputs.profiles }}" test: - needs: get_profiles + needs: [ get_profiles, echo_log ] uses: ./.github/workflows/test-analysis.yml with: test_profile: ${{ needs.get_profiles.outputs.profiles }} From b697f89df8049079691aa41754117a2226e33302 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 23 May 2023 12:39:47 +0200 Subject: [PATCH 044/109] cicd: Adding log #TASK-4445 --- .github/workflows/check-junit-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check-junit-test.yml b/.github/workflows/check-junit-test.yml index 809ce259828..f953642c9eb 100644 --- a/.github/workflows/check-junit-test.yml +++ b/.github/workflows/check-junit-test.yml @@ -25,7 +25,7 @@ jobs: name: Test JUnit runs-on: ubuntu-22.04 outputs: - profile: ${{ steps.getter.outputs.profiles }} + profiles: ${{ steps.getter.outputs.profiles }} steps: - uses: actions/checkout@v3 with: From 7aa5f59dee3e475064556b437376cad63f707202 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 24 May 2023 12:04:45 +0200 Subject: [PATCH 045/109] CICD: fix yml to release tar.gz related with TASK-4406 --- .github/workflows/release.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 5479fc5bb4c..ecd3d4152cf 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -53,9 +53,9 @@ jobs: release: uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop - needs: test - with: - artifact: build-folder - file: | - opencga-client-${{ needs.build.outputs.version }}.tar.gz - clients/R/opencgaR_${{ needs.build.outputs.version }}.tar.gz + needs: [ build,test ] + with: + artifact: build-folder + file: | + opencga-client-${{ needs.build.outputs.version }}.tar.gz + clients/R/opencgaR_${{ needs.build.outputs.version }}.tar.gz From 5bb318a2930ae2b82763c77a35da86899e29499e Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 26 May 2023 16:41:46 +0200 Subject: [PATCH 046/109] Prepare release 2.9.0 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-deps-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp2.6/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 10 +++++----- 21 files changed, 25 insertions(+), 25 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 10184c4d1ae..506063fcbe0 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 4ac72115c89..84aec45ed6e 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 1bded6a828a..b2cf9e69e45 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index cc666ed2646..43b81784554 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 88157b769f9..1c6f99c9da1 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index f8a759696b8..095118e29c5 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 6bcfe1229a1..9ecb60f987d 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 146bfdcb0f1..db21a3db9b2 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 762d12d1730..61e9c98f2d4 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 611100fea78..4c4ad72fb26 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 830a04cf6c9..41d5ba608fe 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -25,7 +25,7 @@ org.opencb.opencga opencga-storage - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 8aefe17d973..3ca2d7747df 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml index 5da87ce97ea..cc833ae07e9 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml index 938346bf05a..6cf4c54ee36 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml index 606c47dea2b..a11f5ffaade 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml index 320691d8782..8a5a59b0204 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml @@ -50,7 +50,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index da7ae969c7d..d83fe46817f 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -28,7 +28,7 @@ org.opencb.opencga opencga-storage - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 4a66ba429de..312e5ee8922 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 8276f52ef48..06934f49948 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 08a12d4c1e6..34ca2e5c727 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/pom.xml b/pom.xml index 437d0956bf5..f3212884ec9 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.0-SNAPSHOT + 2.9.0 pom OpenCGA OenCGA projects implements a big data platform for genomic data analysis @@ -44,10 +44,10 @@ 2.9.0-dev 2.9.0-dev - 5.5.0-SNAPSHOT - 2.9.0-SNAPSHOT - 4.9.0-SNAPSHOT - 2.9.0-SNAPSHOT + 5.5.0 + 2.9.0 + 4.9.0 + 2.9.0 0.2.0 2.11.4 From 6c24152eb724d8b5310ab2a01108a298810319c6 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 26 May 2023 16:51:04 +0200 Subject: [PATCH 047/109] Prepare release 2.9.0 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-deps-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp2.6/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 10 +++++----- 21 files changed, 25 insertions(+), 25 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 10184c4d1ae..506063fcbe0 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 4ac72115c89..84aec45ed6e 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 1bded6a828a..b2cf9e69e45 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index cc666ed2646..43b81784554 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 88157b769f9..1c6f99c9da1 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index f8a759696b8..095118e29c5 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 6bcfe1229a1..9ecb60f987d 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 146bfdcb0f1..db21a3db9b2 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 762d12d1730..61e9c98f2d4 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 611100fea78..4c4ad72fb26 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 830a04cf6c9..41d5ba608fe 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -25,7 +25,7 @@ org.opencb.opencga opencga-storage - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 8aefe17d973..3ca2d7747df 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml index 5da87ce97ea..cc833ae07e9 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml index 938346bf05a..6cf4c54ee36 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml index 606c47dea2b..a11f5ffaade 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml index 320691d8782..8a5a59b0204 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml @@ -50,7 +50,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index da7ae969c7d..d83fe46817f 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -28,7 +28,7 @@ org.opencb.opencga opencga-storage - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 4a66ba429de..312e5ee8922 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 8276f52ef48..06934f49948 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 08a12d4c1e6..34ca2e5c727 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 2.9.0-SNAPSHOT + 2.9.0 ../pom.xml diff --git a/pom.xml b/pom.xml index 437d0956bf5..f3212884ec9 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.0-SNAPSHOT + 2.9.0 pom OpenCGA OenCGA projects implements a big data platform for genomic data analysis @@ -44,10 +44,10 @@ 2.9.0-dev 2.9.0-dev - 5.5.0-SNAPSHOT - 2.9.0-SNAPSHOT - 4.9.0-SNAPSHOT - 2.9.0-SNAPSHOT + 5.5.0 + 2.9.0 + 4.9.0 + 2.9.0 0.2.0 2.11.4 From b65ec96d35d8f0729b85d5e27d851a98a96ebc86 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 26 May 2023 16:52:27 +0200 Subject: [PATCH 048/109] Prepare new development branch release-2.9.x --- .github/workflows/test-analysis.yml | 2 +- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-deps-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp2.6/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 22 files changed, 28 insertions(+), 28 deletions(-) diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index ca38d16c6b3..04b4414e9fe 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -24,7 +24,7 @@ on: SSH_TESTING_SERVER_PASSWORD: required: true env: - xb_version: "1.6.1" + xb_version: "1.7.0" jobs: analysis: name: Execute Sonar Analysis diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 506063fcbe0..ddefa7d2618 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.0 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 84aec45ed6e..c0bc97362b9 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.0 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index b2cf9e69e45..c911504528d 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 2.9.0 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 43b81784554..25c7042ce63 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.0 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 1c6f99c9da1..d7c383eec63 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 2.9.0 + 2.10.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 095118e29c5..b23641a3dbd 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.0 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 9ecb60f987d..d1e079cf6a8 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 2.9.0 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index db21a3db9b2..f16e51062b9 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.0 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 61e9c98f2d4..209b780bb8c 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.9.0 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 4c4ad72fb26..e43034af54f 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 2.9.0 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 41d5ba608fe..95c37c68a8c 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -25,7 +25,7 @@ org.opencb.opencga opencga-storage - 2.9.0 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 3ca2d7747df..ca90d6fc622 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.9.0 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml index cc833ae07e9..001205ea43e 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.9.0 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml index 6cf4c54ee36..e8ed3f367fc 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.9.0 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml index a11f5ffaade..19403f3054e 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.9.0 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml index 8a5a59b0204..f46f425eede 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml @@ -50,7 +50,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.9.0 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index d83fe46817f..d2c588dc56f 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -28,7 +28,7 @@ org.opencb.opencga opencga-storage - 2.9.0 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 312e5ee8922..42703d7ee32 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.9.0 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 06934f49948..643cebae481 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.0 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 34ca2e5c727..18c878e910c 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 2.9.0 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index f3212884ec9..8cd2d21fbe7 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.0 + 2.10.0-SNAPSHOT pom OpenCGA OenCGA projects implements a big data platform for genomic data analysis @@ -42,12 +42,12 @@ - 2.9.0-dev - 2.9.0-dev - 5.5.0 - 2.9.0 - 4.9.0 - 2.9.0 + 2.10.0_dev + 2.10.0_dev + 5.6.0-SNAPSHOT + 2.10.0-SNAPSHOT + 4.10.0-SNAPSHOT + 2.10.0-SNAPSHOT 0.2.0 2.11.4 From dd109d85ab2d7cce791d8df16228e901ba425d49 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 26 May 2023 16:53:05 +0200 Subject: [PATCH 049/109] Prepare new development branch release-2.9.x --- .github/workflows/test-analysis.yml | 2 +- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-deps-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp2.6/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 22 files changed, 28 insertions(+), 28 deletions(-) diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index 04b4414e9fe..7de7dfd920a 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -24,7 +24,7 @@ on: SSH_TESTING_SERVER_PASSWORD: required: true env: - xb_version: "1.7.0" + xb_version: "1.6.2" jobs: analysis: name: Execute Sonar Analysis diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index ddefa7d2618..4e8c931536f 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.10.0-SNAPSHOT + 2.9.1-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index c0bc97362b9..74ab91fb07f 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.10.0-SNAPSHOT + 2.9.1-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index c911504528d..8648dfbb20d 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 2.10.0-SNAPSHOT + 2.9.1-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 25c7042ce63..e58a4f025f9 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.10.0-SNAPSHOT + 2.9.1-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index d7c383eec63..0f3e6be7560 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 2.10.0-SNAPSHOT + 2.9.1-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index b23641a3dbd..2100338ef11 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.10.0-SNAPSHOT + 2.9.1-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index d1e079cf6a8..a3c8e96f61b 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 2.10.0-SNAPSHOT + 2.9.1-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index f16e51062b9..a56bb4e317a 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.10.0-SNAPSHOT + 2.9.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 209b780bb8c..f1f9570dc82 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.10.0-SNAPSHOT + 2.9.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index e43034af54f..a11e3049ea8 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 2.10.0-SNAPSHOT + 2.9.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 95c37c68a8c..3297bd21564 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -25,7 +25,7 @@ org.opencb.opencga opencga-storage - 2.10.0-SNAPSHOT + 2.9.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index ca90d6fc622..ec5b94b1ab0 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.10.0-SNAPSHOT + 2.9.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml index 001205ea43e..69ce1a5ae86 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.10.0-SNAPSHOT + 2.9.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml index e8ed3f367fc..3b7b31cbd1d 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.10.0-SNAPSHOT + 2.9.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml index 19403f3054e..99b707529e7 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.10.0-SNAPSHOT + 2.9.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml index f46f425eede..5a39a152b21 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml @@ -50,7 +50,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.10.0-SNAPSHOT + 2.9.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index d2c588dc56f..6d31451f331 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -28,7 +28,7 @@ org.opencb.opencga opencga-storage - 2.10.0-SNAPSHOT + 2.9.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 42703d7ee32..1d32e52b9d6 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.10.0-SNAPSHOT + 2.9.1-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 643cebae481..1afe2783957 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.10.0-SNAPSHOT + 2.9.1-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 18c878e910c..4fa4cdd08e3 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 2.10.0-SNAPSHOT + 2.9.1-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 8cd2d21fbe7..acaa1b8d962 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.10.0-SNAPSHOT + 2.9.1-SNAPSHOT pom OpenCGA OenCGA projects implements a big data platform for genomic data analysis @@ -42,12 +42,12 @@ - 2.10.0_dev - 2.10.0_dev - 5.6.0-SNAPSHOT - 2.10.0-SNAPSHOT - 4.10.0-SNAPSHOT - 2.10.0-SNAPSHOT + 2.9.1_dev + 2.9.1_dev + 5.5.1-SNAPSHOT + 2.9.1-SNAPSHOT + 4.9.1-SNAPSHOT + 2.9.1-SNAPSHOT 0.2.0 2.11.4 From 461ecc8eb2fe861ef2456e893f23875e698d3ad3 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 26 May 2023 17:05:02 +0200 Subject: [PATCH 050/109] Fix release.yml --- .github/workflows/release.yml | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index ecd3d4152cf..3bb701cba50 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -41,8 +41,6 @@ jobs: cli: python3 ./build/cloud/docker/docker-build.py push --images base,init secrets: inherit - - deploy-python: uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop needs: test @@ -54,8 +52,8 @@ jobs: release: uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop needs: [ build,test ] - with: - artifact: build-folder - file: | - opencga-client-${{ needs.build.outputs.version }}.tar.gz - clients/R/opencgaR_${{ needs.build.outputs.version }}.tar.gz + with: + artifact: build-folder + file: | + opencga-client-${{ needs.build.outputs.version }}.tar.gz + clients/R/opencgaR_${{ needs.build.outputs.version }}.tar.gz From 05d51664917682c7f87449d57739f99e1c686969 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 26 May 2023 17:06:41 +0200 Subject: [PATCH 051/109] Fix release.yml --- .github/workflows/release.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index ecd3d4152cf..87a8f237508 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -54,8 +54,8 @@ jobs: release: uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop needs: [ build,test ] - with: - artifact: build-folder - file: | - opencga-client-${{ needs.build.outputs.version }}.tar.gz - clients/R/opencgaR_${{ needs.build.outputs.version }}.tar.gz + with: + artifact: build-folder + file: | + opencga-client-${{ needs.build.outputs.version }}.tar.gz + clients/R/opencgaR_${{ needs.build.outputs.version }}.tar.gz From 5c8e32236e28ed7bed1776bf176fb0c657f862cc Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 26 May 2023 17:14:53 +0200 Subject: [PATCH 052/109] Fix conflicts --- opencga-analysis/pom.xml | 4 ---- opencga-app/pom.xml | 4 ---- opencga-catalog/pom.xml | 4 ---- opencga-client/pom.xml | 4 ---- opencga-clinical/pom.xml | 4 ---- opencga-core/pom.xml | 4 ---- opencga-master/pom.xml | 4 ---- opencga-server/pom.xml | 4 ---- opencga-storage/opencga-storage-app/pom.xml | 4 ---- opencga-storage/opencga-storage-benchmark/pom.xml | 4 ---- opencga-storage/opencga-storage-core/pom.xml | 4 ---- .../opencga-storage-hadoop-core/pom.xml | 4 ---- .../opencga-storage-hadoop-deps-emr6.1/pom.xml | 4 ---- .../opencga-storage-hadoop-deps-hdp2.6/pom.xml | 4 ---- .../opencga-storage-hadoop-deps-hdp3.1/pom.xml | 4 ---- .../opencga-storage-hadoop-deps/pom.xml | 4 ---- opencga-storage/opencga-storage-hadoop/pom.xml | 4 ---- opencga-storage/opencga-storage-server/pom.xml | 4 ---- opencga-storage/pom.xml | 4 ---- opencga-test/pom.xml | 4 ---- pom.xml | 13 ------------- 21 files changed, 93 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index e537b0bbe32..ddefa7d2618 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,11 +22,7 @@ org.opencb.opencga opencga -<<<<<<< HEAD - 2.9.0 -======= 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index c11d0fefce6..c0bc97362b9 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,11 +22,7 @@ org.opencb.opencga opencga -<<<<<<< HEAD - 2.9.0 -======= 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index e44afd6d960..c911504528d 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,11 +23,7 @@ org.opencb.opencga opencga -<<<<<<< HEAD - 2.9.0 -======= 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 5c574f815f6..25c7042ce63 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,11 +22,7 @@ org.opencb.opencga opencga -<<<<<<< HEAD - 2.9.0 -======= 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 235cccb1df6..d7c383eec63 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,11 +5,7 @@ org.opencb.opencga opencga -<<<<<<< HEAD - 2.9.0 -======= 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 399dc6a6b36..b23641a3dbd 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,11 +22,7 @@ org.opencb.opencga opencga -<<<<<<< HEAD - 2.9.0 -======= 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index d2b44b213eb..d1e079cf6a8 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,11 +22,7 @@ opencga org.opencb.opencga -<<<<<<< HEAD - 2.9.0 -======= 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 41b4d4ee2df..f16e51062b9 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,11 +22,7 @@ org.opencb.opencga opencga -<<<<<<< HEAD - 2.9.0 -======= 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 24a081e8134..209b780bb8c 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,11 +22,7 @@ org.opencb.opencga opencga-storage -<<<<<<< HEAD - 2.9.0 -======= 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index f93c21a4449..e43034af54f 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,11 +22,7 @@ opencga-storage org.opencb.opencga -<<<<<<< HEAD - 2.9.0 -======= 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index aa5318ea6e7..95c37c68a8c 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -25,11 +25,7 @@ org.opencb.opencga opencga-storage -<<<<<<< HEAD - 2.9.0 -======= 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 3553f855e4c..ca90d6fc622 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,11 +23,7 @@ org.opencb.opencga opencga-storage-hadoop -<<<<<<< HEAD - 2.9.0 -======= 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml index a883c9a7421..001205ea43e 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml @@ -22,11 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps -<<<<<<< HEAD - 2.9.0 -======= 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml index a86203ff8cd..e8ed3f367fc 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml @@ -22,11 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps -<<<<<<< HEAD - 2.9.0 -======= 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml index d2d1923dda9..19403f3054e 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml @@ -22,11 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps -<<<<<<< HEAD - 2.9.0 -======= 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml index 280c48971a4..f46f425eede 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml @@ -50,11 +50,7 @@ org.opencb.opencga opencga-storage-hadoop -<<<<<<< HEAD - 2.9.0 -======= 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index cef60a808de..d2c588dc56f 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -28,11 +28,7 @@ org.opencb.opencga opencga-storage -<<<<<<< HEAD - 2.9.0 -======= 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index d570556f9b2..42703d7ee32 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,11 +22,7 @@ org.opencb.opencga opencga-storage -<<<<<<< HEAD - 2.9.0 -======= 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index aea0014cd1e..643cebae481 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,11 +22,7 @@ org.opencb.opencga opencga -<<<<<<< HEAD - 2.9.0 -======= 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 4ae3f80c3d1..18c878e910c 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,11 +24,7 @@ org.opencb.opencga opencga -<<<<<<< HEAD - 2.9.0 -======= 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x ../pom.xml diff --git a/pom.xml b/pom.xml index 2776dfe1fbb..8cd2d21fbe7 100644 --- a/pom.xml +++ b/pom.xml @@ -22,11 +22,7 @@ org.opencb.opencga opencga -<<<<<<< HEAD - 2.9.0 -======= 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x pom OpenCGA OenCGA projects implements a big data platform for genomic data analysis @@ -46,21 +42,12 @@ -<<<<<<< HEAD - 2.9.0-dev - 2.9.0-dev - 5.5.0 - 2.9.0 - 4.9.0 - 2.9.0 -======= 2.10.0_dev 2.10.0_dev 5.6.0-SNAPSHOT 2.10.0-SNAPSHOT 4.10.0-SNAPSHOT 2.10.0-SNAPSHOT ->>>>>>> release-2.9.x 0.2.0 2.11.4 From dfd74656fe9f998ff19be16d5b02d142ed88a3f1 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 26 May 2023 17:15:50 +0200 Subject: [PATCH 053/109] Fix dev versions --- pom.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pom.xml b/pom.xml index f3212884ec9..971db5bdae4 100644 --- a/pom.xml +++ b/pom.xml @@ -42,8 +42,8 @@ - 2.9.0-dev - 2.9.0-dev + 2.9.0 + 2.9.0 5.5.0 2.9.0 4.9.0 From 912aa4840cdbf8ebb8ea1d6ba2fc81515d205207 Mon Sep 17 00:00:00 2001 From: imedina Date: Mon, 29 May 2023 01:33:49 +0100 Subject: [PATCH 054/109] docker: use Ubuntu 22.04 + OpenJDK 8u372 to take advantage of cgroup v2 --- .../app/cloud/docker/opencga-base/Dockerfile | 27 +++++++++++-------- .../app/cloud/docker/opencga-init/Dockerfile | 21 +++++++-------- 2 files changed, 25 insertions(+), 23 deletions(-) diff --git a/opencga-app/app/cloud/docker/opencga-base/Dockerfile b/opencga-app/app/cloud/docker/opencga-base/Dockerfile index 5132720657c..d3eee2266d2 100644 --- a/opencga-app/app/cloud/docker/opencga-base/Dockerfile +++ b/opencga-app/app/cloud/docker/opencga-base/Dockerfile @@ -1,5 +1,6 @@ -## Based on Debian 11 (bullseye) -FROM openjdk:8-jre +## Based on Ubuntu 22.04 (jammy) +## We are now using OpenJDK 8u372 to support "cgroup v2", see https://developers.redhat.com/articles/2023/04/19/openjdk-8u372-feature-cgroup-v2-support# +FROM eclipse-temurin:8u372-b07-jre-jammy ARG BUILD_PATH="." @@ -7,17 +8,21 @@ ENV OPENCGA_HOME=/opt/opencga ENV OPENCGA_CONFIG_DIR=${OPENCGA_HOME}/conf RUN apt-get update && apt-get -y upgrade && apt-get install -y lsb-release sshpass ca-certificates curl gnupg jq ncurses-bin && \ - # Install Docker repository - curl -fsSL https://download.docker.com/linux/debian/gpg | gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg && \ - echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/debian \ - $(lsb_release -cs) stable" | tee /etc/apt/sources.list.d/docker.list > /dev/null && \ - # Install MongoDB repository - wget -qO - https://www.mongodb.org/static/pgp/server-4.2.asc | apt-key add - && \ - echo "deb http://repo.mongodb.org/apt/debian buster/mongodb-org/4.2 main" | tee /etc/apt/sources.list.d/mongodb-org-4.2.list && \ - apt-get update && apt-get install -y docker-ce docker-ce-cli containerd.io mongodb-org-shell && \ - rm -rf /var/lib/apt/lists/* && \ + ## Install Docker repository + install -m 0755 -d /etc/apt/keyrings && \ + curl -fsSL https://download.docker.com/linux/ubuntu/gpg | gpg --dearmor -o /etc/apt/keyrings/docker.gpg && \ + chmod a+r /etc/apt/keyrings/docker.gpg && \ + echo "deb [arch="$(dpkg --print-architecture)" signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/ubuntu "$(. /etc/os-release && echo "jammy")" stable" | tee /etc/apt/sources.list.d/docker.list > /dev/null && \ + ## Install MongoDB 6.0 repository + curl -fsSL https://pgp.mongodb.com/server-6.0.asc | gpg --dearmor -o /usr/share/keyrings/mongodb-server-6.0.gpg && \ + echo "deb [ arch=amd64,arm64 signed-by=/usr/share/keyrings/mongodb-server-6.0.gpg ] https://repo.mongodb.org/apt/ubuntu jammy/mongodb-org/6.0 multiverse" | tee /etc/apt/sources.list.d/mongodb-org-6.0.list && \ + ## Install docker and mongodb packages + apt-get update && apt-get install -y docker-ce docker-ce-cli containerd.io mongodb-mongosh && \ + ## Install yq wget -qO /usr/local/bin/yq https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64 && \ chmod +x /usr/local/bin/yq && \ + ## Clean downloaded packages to make images smaller + rm -rf /var/lib/apt/lists/* && \ adduser --disabled-password --uid 1001 opencga ## Run Docker images as non root diff --git a/opencga-app/app/cloud/docker/opencga-init/Dockerfile b/opencga-app/app/cloud/docker/opencga-init/Dockerfile index f7efd322ac9..60b60f278b7 100644 --- a/opencga-app/app/cloud/docker/opencga-init/Dockerfile +++ b/opencga-app/app/cloud/docker/opencga-init/Dockerfile @@ -8,25 +8,22 @@ ARG INIT_PATH=cloud/docker/opencga-init/ COPY ${INIT_PATH} /opt/opencga/init/ COPY ${BUILD_PATH}/conf/* /opt/opencga/init/test/ - -# Mount volume to copy config into +## Mount volume to copy config into VOLUME /opt/volume USER root -# Install local dependencies -RUN apt install python3 && \ - echo "deb http://ftp.de.debian.org/debian bullseye main" | tee -a /etc/apt/sources.list.d/sources.list && \ - apt-get update && apt-get -y upgrade && \ - apt install -y python3-pip && \ + +## Install local dependencies +RUN apt-get update && apt-get -y upgrade && apt-get install -y python3 python3-pip && \ pip3 install --upgrade pip setuptools && \ pip3 install -r /opt/opencga/init/requirements.txt && \ chmod +x /opt/opencga/init/setup.sh /opt/opencga/init/setup-hadoop.sh && \ echo ">Running init container configuration tests" && \ cd /opt/opencga/init/test && python3 test_override_yaml.py -v && rm -r /opt/opencga/init/test - +## Run Docker images as non root USER opencga -# It is the responsibility of the setup.sh -# script to initialise the volume correctly -# and apply any runtime config transforms. -ENTRYPOINT [ "/bin/sh","/opt/opencga/init/setup.sh" ] + +## It is the responsibility of the setup.sh script to initialise the volume correctly +## and apply any runtime config transforms. +ENTRYPOINT [ "/bin/sh", "/opt/opencga/init/setup.sh" ] From 0e8cde0f2afd7dc888fdb977d7143c871e3aac10 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 13 Jun 2023 15:44:41 +0200 Subject: [PATCH 055/109] Prepare release 2.9.1 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-deps-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp2.6/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 21 files changed, 27 insertions(+), 27 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 4e8c931536f..ed6d1e6ea9c 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.1-SNAPSHOT + 2.9.1 ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 74ab91fb07f..ddac6242b5a 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.1-SNAPSHOT + 2.9.1 ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 8648dfbb20d..4bd331c20cd 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 2.9.1-SNAPSHOT + 2.9.1 ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index e58a4f025f9..3b99ea89a10 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.1-SNAPSHOT + 2.9.1 ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 0f3e6be7560..70f90af19bf 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 2.9.1-SNAPSHOT + 2.9.1 ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 2100338ef11..5b526af39c5 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.1-SNAPSHOT + 2.9.1 ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index a3c8e96f61b..097227b48fb 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 2.9.1-SNAPSHOT + 2.9.1 ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index a56bb4e317a..c1dedc8f9b5 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.1-SNAPSHOT + 2.9.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index f1f9570dc82..3866f9663c5 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.9.1-SNAPSHOT + 2.9.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index a11e3049ea8..efca71394d9 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 2.9.1-SNAPSHOT + 2.9.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 3297bd21564..5d72ad07bd9 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -25,7 +25,7 @@ org.opencb.opencga opencga-storage - 2.9.1-SNAPSHOT + 2.9.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index ec5b94b1ab0..e0e24254c4d 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.9.1-SNAPSHOT + 2.9.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml index 69ce1a5ae86..3263e91216a 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.9.1-SNAPSHOT + 2.9.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml index 3b7b31cbd1d..efc599af6fb 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.9.1-SNAPSHOT + 2.9.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml index 99b707529e7..64bfaffce10 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.9.1-SNAPSHOT + 2.9.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml index 5a39a152b21..59b617f558b 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml @@ -50,7 +50,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.9.1-SNAPSHOT + 2.9.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 6d31451f331..c1e722996de 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -28,7 +28,7 @@ org.opencb.opencga opencga-storage - 2.9.1-SNAPSHOT + 2.9.1 ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 1d32e52b9d6..323e4ef2404 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.9.1-SNAPSHOT + 2.9.1 ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 1afe2783957..80340a628c9 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.1-SNAPSHOT + 2.9.1 ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 4fa4cdd08e3..a7ff7fcb5cb 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 2.9.1-SNAPSHOT + 2.9.1 ../pom.xml diff --git a/pom.xml b/pom.xml index 5a247d5b293..7740e246360 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.1-SNAPSHOT + 2.9.1 pom OpenCGA OenCGA projects implements a big data platform for genomic data analysis @@ -42,12 +42,12 @@ - 2.9.1_dev - 2.9.1_dev - 5.5.1-SNAPSHOT - 2.9.1-SNAPSHOT - 4.9.1-SNAPSHOT - 2.9.1-SNAPSHOT + 2.9.1 + 2.9.1 + 5.5.0 + 2.9.0 + 4.9.0 + 2.9.1 0.2.0 2.11.4 From 548c19fad1df0b8745850b904e99d12b2a33fcfb Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 13 Jun 2023 15:54:17 +0200 Subject: [PATCH 056/109] Prepare next release 2.9.2-SNAPSHOT --- .github/workflows/test-analysis.yml | 3 +-- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-deps-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp2.6/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 22 files changed, 28 insertions(+), 29 deletions(-) diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index ac937f35c4c..b778e704cae 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -24,8 +24,7 @@ on: SSH_TESTING_SERVER_PASSWORD: required: true env: - xb_version: "1.7.1" - + xb_version: "1.7.2" jobs: analysis: name: Execute Sonar Analysis diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index ed6d1e6ea9c..aec5669b12f 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.1 + 2.9.2-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index ddac6242b5a..a9fe3703f97 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.1 + 2.9.2-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 4bd331c20cd..43fb05be14d 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 2.9.1 + 2.9.2-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 3b99ea89a10..bed3ac24829 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.1 + 2.9.2-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 70f90af19bf..9f85a0ff7d0 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 2.9.1 + 2.9.2-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 5b526af39c5..8544e3bbd09 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.1 + 2.9.2-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 097227b48fb..898205375bc 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 2.9.1 + 2.9.2-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index c1dedc8f9b5..957eb127745 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.1 + 2.9.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 3866f9663c5..45bd1dd22c1 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.9.1 + 2.9.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index efca71394d9..cdd5e80590b 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 2.9.1 + 2.9.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 5d72ad07bd9..ab277249b74 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -25,7 +25,7 @@ org.opencb.opencga opencga-storage - 2.9.1 + 2.9.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index e0e24254c4d..2ef22a0bf03 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.9.1 + 2.9.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml index 3263e91216a..6ed975a82d8 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.9.1 + 2.9.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml index efc599af6fb..422fa4f30c2 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.9.1 + 2.9.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml index 64bfaffce10..a2e8db3647b 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.9.1 + 2.9.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml index 59b617f558b..246bdd0cc61 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml @@ -50,7 +50,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.9.1 + 2.9.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index c1e722996de..e7302b47a65 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -28,7 +28,7 @@ org.opencb.opencga opencga-storage - 2.9.1 + 2.9.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 323e4ef2404..580e03d7ebc 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.9.1 + 2.9.2-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 80340a628c9..eff64556c36 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.1 + 2.9.2-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index a7ff7fcb5cb..6b0e2013c39 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 2.9.1 + 2.9.2-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 7740e246360..d8b1fd7308a 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.1 + 2.9.2-SNAPSHOT pom OpenCGA OenCGA projects implements a big data platform for genomic data analysis @@ -42,12 +42,12 @@ - 2.9.1 - 2.9.1 - 5.5.0 - 2.9.0 - 4.9.0 - 2.9.1 + 2.9.2_dev + 2.9.2_dev + 5.5.1-SNAPSHOT + 2.9.1-SNAPSHOT + 4.9.1-SNAPSHOT + 2.9.2-SNAPSHOT 0.2.0 2.11.4 From 020d2f9e1f33866d4dca120d5e68e6ec2faedaf1 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 13 Jun 2023 16:12:46 +0200 Subject: [PATCH 057/109] Fix release.yml --- .github/workflows/release.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index b5d1f3b7398..388e4aacf92 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -54,9 +54,9 @@ jobs: release: uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@release-4.9.x needs: [ build,test ] - with: - artifact: build-folder - file: | - opencga-client-${{ needs.build.outputs.version }}.tar.gz - clients/R/opencgaR_${{ needs.build.outputs.version }}.tar.gz + with: + artifact: build-folder + file: | + opencga-client-${{ needs.build.outputs.version }}.tar.gz + clients/R/opencgaR_${{ needs.build.outputs.version }}.tar.gz From a7d2143f567bee0ca12ca7f9f6627a6693d32ff1 Mon Sep 17 00:00:00 2001 From: imedina Date: Mon, 19 Jun 2023 00:58:01 +0100 Subject: [PATCH 058/109] cicd: remove docker ext-tools creation from develop and release workflows --- .github/workflows/develop.yml | 12 ++++++------ .../{docker-tools.yml => docker-ext-tools.yml} | 6 +++--- .github/workflows/release.yml | 12 ++++++------ .github/workflows/task.yml | 3 ++- 4 files changed, 17 insertions(+), 16 deletions(-) rename .github/workflows/{docker-tools.yml => docker-ext-tools.yml} (90%) diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml index 6577a417189..94ced2c7296 100644 --- a/.github/workflows/develop.yml +++ b/.github/workflows/develop.yml @@ -13,12 +13,12 @@ jobs: with: maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' - deploy-docker-ext-tools: - uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x - needs: build - with: - cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }} - secrets: inherit +# deploy-docker-ext-tools: +# uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x +# needs: build +# with: +# cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }} +# secrets: inherit test: uses: ./.github/workflows/test-analysis.yml diff --git a/.github/workflows/docker-tools.yml b/.github/workflows/docker-ext-tools.yml similarity index 90% rename from .github/workflows/docker-tools.yml rename to .github/workflows/docker-ext-tools.yml index d4b80e913e4..b1fd5005436 100644 --- a/.github/workflows/docker-tools.yml +++ b/.github/workflows/docker-ext-tools.yml @@ -1,4 +1,4 @@ -name: Deploy Docker Tools +name: Deploy Docker Ext-Tools on: push: @@ -13,8 +13,8 @@ on: jobs: build: uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.9.x - with: - maven_opts: +# with: +# maven_opts: deploy-docker-ext-tools: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 0fb1f666a62..adcf2f27a56 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -12,12 +12,12 @@ jobs: with: maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' - deploy-docker-ext-tools: - uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x - needs: build - with: - cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }} - secrets: inherit +# deploy-docker-ext-tools: +# uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x +# needs: build +# with: +# cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }} +# secrets: inherit test: uses: ./.github/workflows/test-analysis.yml diff --git a/.github/workflows/task.yml b/.github/workflows/task.yml index d48509a97df..169993bf4c9 100644 --- a/.github/workflows/task.yml +++ b/.github/workflows/task.yml @@ -5,7 +5,8 @@ on: branches: - TASK-* workflow_dispatch: -#WARNING Develop branch needed for prod + +# WARNING Develop branch needed for prod jobs: build: uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.9.x From 37ffe01c5646f2cf6643aca5f74d4f1e91cd17d9 Mon Sep 17 00:00:00 2001 From: imedina Date: Mon, 19 Jun 2023 01:01:25 +0100 Subject: [PATCH 059/109] cicd: testin new docker ext-tools creation workflow --- opencga-app/app/cloud/docker/opencga-ext-tools/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/opencga-app/app/cloud/docker/opencga-ext-tools/Dockerfile b/opencga-app/app/cloud/docker/opencga-ext-tools/Dockerfile index 024f4ed2a68..1ee9b95fdee 100644 --- a/opencga-app/app/cloud/docker/opencga-ext-tools/Dockerfile +++ b/opencga-app/app/cloud/docker/opencga-ext-tools/Dockerfile @@ -30,4 +30,4 @@ RUN apt-get update -y && DEBIAN_FRONTEND="noninteractive" TZ="Europe/London" apt rm -rf /var/lib/apt/lists/* /tmp/* /opt/opencga/signature.tools.lib/.git && \ strip --remove-section=.note.ABI-tag /usr/lib/x86_64-linux-gnu/libQt5Core.so.5 -WORKDIR /opt/opencga \ No newline at end of file +WORKDIR /opt/opencga From 05aabd1796e39aff2c7a0a4833bbf5647def8c19 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 19 Jun 2023 12:31:13 +0200 Subject: [PATCH 060/109] CICD: Test phase commented #TASK-4464 --- .github/workflows/develop.yml | 14 +++--- .github/workflows/docker-aws-emr.yml | 4 +- .github/workflows/docker-tools.yml | 14 +++--- .github/workflows/long-test-analysis.yml | 22 ++++----- .github/workflows/pull-request-merge.yml | 2 +- .github/workflows/release.yml | 18 +++---- .github/workflows/task.yml | 10 ++-- .github/workflows/test-analysis.yml | 63 ++++++++++++++---------- 8 files changed, 79 insertions(+), 68 deletions(-) diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml index 6577a417189..ab685322beb 100644 --- a/.github/workflows/develop.yml +++ b/.github/workflows/develop.yml @@ -9,12 +9,12 @@ on: jobs: build: - uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop with: maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' deploy-docker-ext-tools: - uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: build with: cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }} @@ -24,19 +24,19 @@ jobs: uses: ./.github/workflows/test-analysis.yml needs: deploy-docker-ext-tools secrets: inherit - with: - test_profile: runShortTests,runMediumTests - report_context: development +# with: +# test_profile: runShortTests,runMediumTests +# report_context: development deploy-maven: - uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop needs: test with: maven_opts: -P storage-hadoop,hdp3.1 -Dopencga.war.name=opencga secrets: inherit deploy-docker: - uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: test with: cli: python3 ./build/cloud/docker/docker-build.py push --images base,init diff --git a/.github/workflows/docker-aws-emr.yml b/.github/workflows/docker-aws-emr.yml index b5bae3ed5ed..bf1c8571ca8 100644 --- a/.github/workflows/docker-aws-emr.yml +++ b/.github/workflows/docker-aws-emr.yml @@ -8,12 +8,12 @@ on: jobs: build: - uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop with: maven_opts: -P storage-hadoop,emr6.1 -Dopencga.war.name=opencga deploy-docker: - uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: build with: cli: python3 ./build/cloud/docker/docker-build.py push --images base,init diff --git a/.github/workflows/docker-tools.yml b/.github/workflows/docker-tools.yml index d4b80e913e4..628b28612cc 100644 --- a/.github/workflows/docker-tools.yml +++ b/.github/workflows/docker-tools.yml @@ -12,13 +12,13 @@ on: jobs: build: - uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop with: maven_opts: - deploy-docker-ext-tools: - uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x - needs: build - with: - cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }} - secrets: inherit +# deploy-docker-ext-tools: +# uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop +# needs: build +# with: +# cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }} +# secrets: inherit diff --git a/.github/workflows/long-test-analysis.yml b/.github/workflows/long-test-analysis.yml index f516eb25029..f17400da032 100644 --- a/.github/workflows/long-test-analysis.yml +++ b/.github/workflows/long-test-analysis.yml @@ -1,15 +1,15 @@ name: Long test for run only on weekend #Every Saturday at 01:10 -on: - schedule: - - cron: '10 1 * * 6' - -jobs: - test: - uses: ./.github/workflows/test-analysis.yml - secrets: inherit - with: - test_profile: runLongTests,runMediumTests,runShortTests - report_context: development +#on: +# schedule: +# - cron: '10 1 * * 6' +# +#jobs: +# test: +# uses: ./.github/workflows/test-analysis.yml +# secrets: inherit +# with: +# test_profile: runLongTests,runMediumTests,runShortTests +# report_context: development diff --git a/.github/workflows/pull-request-merge.yml b/.github/workflows/pull-request-merge.yml index 54a63c56149..4b1c43c682b 100644 --- a/.github/workflows/pull-request-merge.yml +++ b/.github/workflows/pull-request-merge.yml @@ -10,7 +10,7 @@ on: jobs: delete-docker: - uses: opencb/java-common-libs/.github/workflows/delete-docker-hub-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/delete-docker-hub-workflow.yml@develop with: cli: python3 ./build/cloud/docker/docker-build.py delete --images base --tag ${{ github.head_ref }} secrets: inherit diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 0fb1f666a62..7235c1e93ee 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -8,12 +8,12 @@ on: jobs: build: - uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop with: maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' deploy-docker-ext-tools: - uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: build with: cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }} @@ -23,26 +23,26 @@ jobs: uses: ./.github/workflows/test-analysis.yml needs: deploy-docker-ext-tools secrets: inherit - with: - test_profile: runShortTests,runMediumTests - report_context: xetabase +# with: +# test_profile: runShortTests,runMediumTests +# report_context: xetabase deploy-maven: - uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop needs: test with: maven_opts: -P storage-hadoop,hdp3.1 -Dopencga.war.name=opencga secrets: inherit deploy-docker: - uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: test with: cli: python3 ./build/cloud/docker/docker-build.py push --images base,init secrets: inherit deploy-python: - uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop needs: test with: cli: ./clients/python/python-build.sh push @@ -50,7 +50,7 @@ jobs: secrets: inherit release: - uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop needs: [ build,test ] with: artifact: build-folder diff --git a/.github/workflows/task.yml b/.github/workflows/task.yml index d48509a97df..775e87e77b7 100644 --- a/.github/workflows/task.yml +++ b/.github/workflows/task.yml @@ -8,7 +8,7 @@ on: #WARNING Develop branch needed for prod jobs: build: - uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop with: maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' @@ -16,12 +16,12 @@ jobs: uses: ./.github/workflows/test-analysis.yml needs: build secrets: inherit - with: - test_profile: runShortTests - report_context: development +# with: +# test_profile: runShortTests +# report_context: development deploy-docker: - uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: test with: cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ github.ref_name }} diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index ac937f35c4c..bd06a020e87 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -83,30 +83,41 @@ jobs: mongodb-replica-set: rs-test - name: Run Junit tests run: mvn -B verify surefire-report:report -P storage-hadoop,hdp3.1,${{ inputs.test_profile }} -Dcheckstyle.skip -Popencga-storage-hadoop-deps -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' ${{ inputs.mvn_opts }} - - name: Upload result dir - uses: actions/upload-artifact@v3 + - name: Publish Test Report + uses: scacap/action-surefire-report@v1 + ## Skip cancelled() + ## https://docs.github.com/en/actions/learn-github-actions/expressions#cancelled + if: success() || failure() with: - name: workdir - path: "**/target/site" - publish-test: - name: Publish test results - runs-on: ubuntu-22.04 - needs: test - strategy: - matrix: - module: ["opencga-app", "opencga-catalog", "opencga-client", "opencga-clinical", "opencga-core", "opencga-master", "opencga-server", "opencga-storage", "opencga-storage/opencga-storage-app", "opencga-storage/opencga-storage-benchmark", "opencga-storage/opencga-storage-core", "opencga-storage/opencga-storage-hadoop", "opencga-storage/opencga-storage-server", "opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core", "opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps"] - steps: - - name: Download result dir - uses: actions/download-artifact@v3 - with: - name: workdir - - name: Deploy unit tests web recursively to remote - uses: garygrossgarten/github-action-scp@release - with: - local: ${{ matrix.module }}/target/site - remote: /var/www/html/reports/${{ inputs.report_context }}/${{ env.xb_version }}/${{ github.ref_name }}/opencga/${{ github.sha }}/unit/${{ matrix.module }} - host: ${{ secrets.SSH_TESTING_SERVER_HOST}} - port: ${{ secrets.SSH_TESTING_SERVER_PORT}} - username: ${{ secrets.SSH_TESTING_SERVER_USER }} - password: ${{ secrets.SSH_TESTING_SERVER_PASSWORD }} - concurrency: 2 + check_name: "Surefire tests report" + report_paths: './**/surefire-reports/TEST-*.xml' + commit: '${{ github.sha }}' + fail_on_test_failures: true + +# - name: Upload result dir +# uses: actions/upload-artifact@v3 +# with: +# name: workdir +# path: "**/target/site" +# publish-test: +# name: Publish test results +# runs-on: ubuntu-22.04 +# needs: test +# strategy: +# matrix: +# module: ["opencga-app", "opencga-catalog", "opencga-client", "opencga-clinical", "opencga-core", "opencga-master", "opencga-server", "opencga-storage", "opencga-storage/opencga-storage-app", "opencga-storage/opencga-storage-benchmark", "opencga-storage/opencga-storage-core", "opencga-storage/opencga-storage-hadoop", "opencga-storage/opencga-storage-server", "opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core", "opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps"] +# steps: +# - name: Download result dir +# uses: actions/download-artifact@v3 +# with: +# name: workdir +# - name: Deploy unit tests web recursively to remote +# uses: garygrossgarten/github-action-scp@release +# with: +# local: ${{ matrix.module }}/target/site +# remote: /var/www/html/reports/${{ inputs.report_context }}/${{ env.xb_version }}/${{ github.ref_name }}/opencga/${{ github.sha }}/unit/${{ matrix.module }} +# host: ${{ secrets.SSH_TESTING_SERVER_HOST}} +# port: ${{ secrets.SSH_TESTING_SERVER_PORT}} +# username: ${{ secrets.SSH_TESTING_SERVER_USER }} +# password: ${{ secrets.SSH_TESTING_SERVER_PASSWORD }} +# concurrency: 2 From d9ee6b94c574944549752e5ce439c7d589bb1a7c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 19 Jun 2023 13:48:58 +0200 Subject: [PATCH 061/109] updated maven-surefire-plugin.version --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index d8b1fd7308a..f36ef9ca58a 100644 --- a/pom.xml +++ b/pom.xml @@ -84,7 +84,7 @@ false false - 2.22.2 + 3.1.0 From 3a5666a24bfc038b2305b1ae7b342693fd06e85d Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 19 Jun 2023 13:49:47 +0200 Subject: [PATCH 062/109] updated maven-surefire-plugin.version --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 003a1f26fe3..8d23566bf5c 100644 --- a/pom.xml +++ b/pom.xml @@ -84,7 +84,7 @@ false false - 2.22.2 + 3.1.0 From 4dc6a24c6a66c0f796a514c4ce9dfa1752fbdf65 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 22 Jun 2023 18:29:04 +0200 Subject: [PATCH 063/109] cicd: Comment test report update code #TASK-4464 --- .github/workflows/test-analysis.yml | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index bd06a020e87..5e97eeca344 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -5,9 +5,9 @@ on: test_profile: type: string required: true - report_context: - type: string - required: true +# report_context: +# type: string +# required: true mvn_opts: type: string required: false @@ -15,16 +15,16 @@ on: secrets: SONAR_TOKEN: required: true - SSH_TESTING_SERVER_HOST: - required: true - SSH_TESTING_SERVER_PORT: - required: true - SSH_TESTING_SERVER_USER: - required: true - SSH_TESTING_SERVER_PASSWORD: - required: true -env: - xb_version: "1.7.1" +# SSH_TESTING_SERVER_HOST: +# required: true +# SSH_TESTING_SERVER_PORT: +# required: true +# SSH_TESTING_SERVER_USER: +# required: true +# SSH_TESTING_SERVER_PASSWORD: +# required: true +#env: +# xb_version: "1.7.1" jobs: analysis: From 48b7e4e7cd68d3c289e7efb9816232d1fb501ace Mon Sep 17 00:00:00 2001 From: imedina Date: Fri, 23 Jun 2023 01:28:04 +0100 Subject: [PATCH 064/109] cicd: minor style improvements --- .github/workflows/develop.yml | 3 -- .github/workflows/docker-tools.yml | 7 ----- .github/workflows/release.yml | 3 -- .github/workflows/task.yml | 4 +-- .github/workflows/test-analysis.yml | 43 ++--------------------------- 5 files changed, 3 insertions(+), 57 deletions(-) diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml index ab685322beb..9d3a1cfd04c 100644 --- a/.github/workflows/develop.yml +++ b/.github/workflows/develop.yml @@ -24,9 +24,6 @@ jobs: uses: ./.github/workflows/test-analysis.yml needs: deploy-docker-ext-tools secrets: inherit -# with: -# test_profile: runShortTests,runMediumTests -# report_context: development deploy-maven: uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop diff --git a/.github/workflows/docker-tools.yml b/.github/workflows/docker-tools.yml index 628b28612cc..1847c1ffccb 100644 --- a/.github/workflows/docker-tools.yml +++ b/.github/workflows/docker-tools.yml @@ -15,10 +15,3 @@ jobs: uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop with: maven_opts: - -# deploy-docker-ext-tools: -# uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop -# needs: build -# with: -# cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }} -# secrets: inherit diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 7235c1e93ee..15d447b3969 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -23,9 +23,6 @@ jobs: uses: ./.github/workflows/test-analysis.yml needs: deploy-docker-ext-tools secrets: inherit -# with: -# test_profile: runShortTests,runMediumTests -# report_context: xetabase deploy-maven: uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop diff --git a/.github/workflows/task.yml b/.github/workflows/task.yml index 775e87e77b7..59d093f7dd3 100644 --- a/.github/workflows/task.yml +++ b/.github/workflows/task.yml @@ -5,6 +5,7 @@ on: branches: - TASK-* workflow_dispatch: + #WARNING Develop branch needed for prod jobs: build: @@ -16,9 +17,6 @@ jobs: uses: ./.github/workflows/test-analysis.yml needs: build secrets: inherit -# with: -# test_profile: runShortTests -# report_context: development deploy-docker: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index 5e97eeca344..2cf07e5c5f1 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -1,13 +1,11 @@ name: Build and test the project + on: workflow_call: inputs: test_profile: type: string required: true -# report_context: -# type: string -# required: true mvn_opts: type: string required: false @@ -15,16 +13,6 @@ on: secrets: SONAR_TOKEN: required: true -# SSH_TESTING_SERVER_HOST: -# required: true -# SSH_TESTING_SERVER_PORT: -# required: true -# SSH_TESTING_SERVER_USER: -# required: true -# SSH_TESTING_SERVER_PASSWORD: -# required: true -#env: -# xb_version: "1.7.1" jobs: analysis: @@ -53,6 +41,7 @@ jobs: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Needed to get PR information, if any SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} run: mvn -T 2 clean install -P storage-hadoop,hdp3.1,${{ inputs.test_profile }} -DskipTests -Dcheckstyle.skip org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=opencb_opencga + test: name: Execute JUnit and Jacoco tests runs-on: ubuntu-22.04 @@ -93,31 +82,3 @@ jobs: report_paths: './**/surefire-reports/TEST-*.xml' commit: '${{ github.sha }}' fail_on_test_failures: true - -# - name: Upload result dir -# uses: actions/upload-artifact@v3 -# with: -# name: workdir -# path: "**/target/site" -# publish-test: -# name: Publish test results -# runs-on: ubuntu-22.04 -# needs: test -# strategy: -# matrix: -# module: ["opencga-app", "opencga-catalog", "opencga-client", "opencga-clinical", "opencga-core", "opencga-master", "opencga-server", "opencga-storage", "opencga-storage/opencga-storage-app", "opencga-storage/opencga-storage-benchmark", "opencga-storage/opencga-storage-core", "opencga-storage/opencga-storage-hadoop", "opencga-storage/opencga-storage-server", "opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core", "opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps"] -# steps: -# - name: Download result dir -# uses: actions/download-artifact@v3 -# with: -# name: workdir -# - name: Deploy unit tests web recursively to remote -# uses: garygrossgarten/github-action-scp@release -# with: -# local: ${{ matrix.module }}/target/site -# remote: /var/www/html/reports/${{ inputs.report_context }}/${{ env.xb_version }}/${{ github.ref_name }}/opencga/${{ github.sha }}/unit/${{ matrix.module }} -# host: ${{ secrets.SSH_TESTING_SERVER_HOST}} -# port: ${{ secrets.SSH_TESTING_SERVER_PORT}} -# username: ${{ secrets.SSH_TESTING_SERVER_USER }} -# password: ${{ secrets.SSH_TESTING_SERVER_PASSWORD }} -# concurrency: 2 From a0eb1af9748604fc32dded27cecb61bb7f8a6ca2 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 23 Jun 2023 13:16:30 +0200 Subject: [PATCH 065/109] cicd: Set the test_profile and fail-never in test #TASK-4464 --- .github/workflows/check-junit-test.yml | 1 - .github/workflows/develop.yml | 2 ++ .github/workflows/release.yml | 5 ----- .github/workflows/task.yml | 2 ++ .github/workflows/test-analysis.yml | 2 +- 5 files changed, 5 insertions(+), 7 deletions(-) diff --git a/.github/workflows/check-junit-test.yml b/.github/workflows/check-junit-test.yml index f953642c9eb..4331f156cf5 100644 --- a/.github/workflows/check-junit-test.yml +++ b/.github/workflows/check-junit-test.yml @@ -51,6 +51,5 @@ jobs: uses: ./.github/workflows/test-analysis.yml with: test_profile: ${{ needs.get_profiles.outputs.profiles }} - report_context: development mvn_opts: ${{ inputs.mvn_opts }} secrets: inherit \ No newline at end of file diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml index 9d3a1cfd04c..d480e5b40a8 100644 --- a/.github/workflows/develop.yml +++ b/.github/workflows/develop.yml @@ -24,6 +24,8 @@ jobs: uses: ./.github/workflows/test-analysis.yml needs: deploy-docker-ext-tools secrets: inherit + with: + test_profile: runShortTests,runMediumTests deploy-maven: uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 15d447b3969..124be6733d6 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -19,11 +19,6 @@ jobs: cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }} secrets: inherit - test: - uses: ./.github/workflows/test-analysis.yml - needs: deploy-docker-ext-tools - secrets: inherit - deploy-maven: uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop needs: test diff --git a/.github/workflows/task.yml b/.github/workflows/task.yml index 59d093f7dd3..68b22b50dc8 100644 --- a/.github/workflows/task.yml +++ b/.github/workflows/task.yml @@ -17,6 +17,8 @@ jobs: uses: ./.github/workflows/test-analysis.yml needs: build secrets: inherit + with: + test_profile: runShortTests deploy-docker: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index 2cf07e5c5f1..732d92a4e56 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -71,7 +71,7 @@ jobs: mongodb-version: 6.0 mongodb-replica-set: rs-test - name: Run Junit tests - run: mvn -B verify surefire-report:report -P storage-hadoop,hdp3.1,${{ inputs.test_profile }} -Dcheckstyle.skip -Popencga-storage-hadoop-deps -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' ${{ inputs.mvn_opts }} + run: mvn -B verify surefire-report:report --fail-never -P storage-hadoop,hdp3.1,${{ inputs.test_profile }} -Dcheckstyle.skip -Popencga-storage-hadoop-deps -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' ${{ inputs.mvn_opts }} - name: Publish Test Report uses: scacap/action-surefire-report@v1 ## Skip cancelled() From c18bc8a49ae24b26ddcca54206ac89899aaaff01 Mon Sep 17 00:00:00 2001 From: imedina Date: Sun, 25 Jun 2023 02:10:01 +0100 Subject: [PATCH 066/109] cicd: minor code style improvement --- .github/workflows/develop.yml | 2 +- .github/workflows/release.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml index d480e5b40a8..fa5a1a1449e 100644 --- a/.github/workflows/develop.yml +++ b/.github/workflows/develop.yml @@ -23,9 +23,9 @@ jobs: test: uses: ./.github/workflows/test-analysis.yml needs: deploy-docker-ext-tools - secrets: inherit with: test_profile: runShortTests,runMediumTests + secrets: inherit deploy-maven: uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 124be6733d6..c4149ecf7d2 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -43,7 +43,7 @@ jobs: release: uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop - needs: [ build,test ] + needs: [ build, test ] with: artifact: build-folder file: | From c978aef14ab3ee57b2ec553e6a33b15a5ce47458 Mon Sep 17 00:00:00 2001 From: imedina Date: Sun, 25 Jun 2023 02:14:47 +0100 Subject: [PATCH 067/109] cicd: fix release.yml --- .github/workflows/release.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index c4149ecf7d2..9374b55147d 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -43,7 +43,7 @@ jobs: release: uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop - needs: [ build, test ] + needs: [ build, deploy-maven, deploy-docker, deploy-python ] with: artifact: build-folder file: | From e10c9924df39fcc7e23cf355ba9e4b6f62f1329f Mon Sep 17 00:00:00 2001 From: imedina Date: Sun, 25 Jun 2023 02:45:11 +0100 Subject: [PATCH 068/109] cicd: code clean-up --- .github/workflows/release.yml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index adcf2f27a56..0dc096c34d4 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -12,13 +12,6 @@ jobs: with: maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' -# deploy-docker-ext-tools: -# uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x -# needs: build -# with: -# cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }} -# secrets: inherit - test: uses: ./.github/workflows/test-analysis.yml needs: deploy-docker-ext-tools From 1b91d849beafbaf685924bea5f9ffaf18d546d0b Mon Sep 17 00:00:00 2001 From: imedina Date: Thu, 29 Jun 2023 08:29:33 +0100 Subject: [PATCH 069/109] cicd: clean workflows --- .github/workflows/develop.yml | 13 +++---------- .github/workflows/docker-aws-emr.yml | 2 -- .github/workflows/docker-ext-tools.yml | 2 -- .github/workflows/long-test-analysis.yml | 2 +- .github/workflows/pull-request-merge.yml | 4 ++-- .github/workflows/release.yml | 10 +++++----- .github/workflows/task.yml | 4 ++-- 7 files changed, 13 insertions(+), 24 deletions(-) diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml index 94ced2c7296..d3c477cb585 100644 --- a/.github/workflows/develop.yml +++ b/.github/workflows/develop.yml @@ -9,17 +9,10 @@ on: jobs: build: - uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop with: maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' -# deploy-docker-ext-tools: -# uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x -# needs: build -# with: -# cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }} -# secrets: inherit - test: uses: ./.github/workflows/test-analysis.yml needs: deploy-docker-ext-tools @@ -29,14 +22,14 @@ jobs: report_context: development deploy-maven: - uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop needs: test with: maven_opts: -P storage-hadoop,hdp3.1 -Dopencga.war.name=opencga secrets: inherit deploy-docker: - uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: test with: cli: python3 ./build/cloud/docker/docker-build.py push --images base,init diff --git a/.github/workflows/docker-aws-emr.yml b/.github/workflows/docker-aws-emr.yml index b5bae3ed5ed..d437c7b5d6f 100644 --- a/.github/workflows/docker-aws-emr.yml +++ b/.github/workflows/docker-aws-emr.yml @@ -18,5 +18,3 @@ jobs: with: cli: python3 ./build/cloud/docker/docker-build.py push --images base,init secrets: inherit -# DOCKER_HUB_USER: ${{ secrets.DOCKER_HUB_USER }} -# DOCKER_HUB_PASSWORD: ${{ secrets.DOCKER_HUB_PASSWORD }} diff --git a/.github/workflows/docker-ext-tools.yml b/.github/workflows/docker-ext-tools.yml index b1fd5005436..7f78ec05737 100644 --- a/.github/workflows/docker-ext-tools.yml +++ b/.github/workflows/docker-ext-tools.yml @@ -13,8 +13,6 @@ on: jobs: build: uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.9.x -# with: -# maven_opts: deploy-docker-ext-tools: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x diff --git a/.github/workflows/long-test-analysis.yml b/.github/workflows/long-test-analysis.yml index f516eb25029..3a56faf6339 100644 --- a/.github/workflows/long-test-analysis.yml +++ b/.github/workflows/long-test-analysis.yml @@ -1,6 +1,6 @@ name: Long test for run only on weekend -#Every Saturday at 01:10 +## Every Saturday at 01:10 on: schedule: - cron: '10 1 * * 6' diff --git a/.github/workflows/pull-request-merge.yml b/.github/workflows/pull-request-merge.yml index 54a63c56149..41ecfb73141 100644 --- a/.github/workflows/pull-request-merge.yml +++ b/.github/workflows/pull-request-merge.yml @@ -3,8 +3,8 @@ name: "Pull Request Merge Workflow" on: pull_request: branches: - - "develop" - - "release-*" + - develop + - release-* types: - closed diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 0dc096c34d4..d110de0c080 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -8,7 +8,7 @@ on: jobs: build: - uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop with: maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' @@ -21,21 +21,21 @@ jobs: report_context: xetabase deploy-maven: - uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop needs: test with: maven_opts: -P storage-hadoop,hdp3.1 -Dopencga.war.name=opencga secrets: inherit deploy-docker: - uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: test with: cli: python3 ./build/cloud/docker/docker-build.py push --images base,init secrets: inherit deploy-python: - uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop needs: test with: cli: ./clients/python/python-build.sh push @@ -43,7 +43,7 @@ jobs: secrets: inherit release: - uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop needs: [ build,test ] with: artifact: build-folder diff --git a/.github/workflows/task.yml b/.github/workflows/task.yml index 169993bf4c9..08c1ec937bc 100644 --- a/.github/workflows/task.yml +++ b/.github/workflows/task.yml @@ -9,7 +9,7 @@ on: # WARNING Develop branch needed for prod jobs: build: - uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop with: maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' @@ -22,7 +22,7 @@ jobs: report_context: development deploy-docker: - uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.9.x + uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: test with: cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ github.ref_name }} From 9aa9345e4613f1eab9a7b029ec65a629613ea436 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Thu, 6 Jul 2023 12:57:02 +0100 Subject: [PATCH 070/109] storage: Add exec command to HBaseMain #TASK-4372 --- .../storage/hadoop/app/AbstractMain.java | 48 ++++++-- .../opencga/storage/hadoop/app/HBaseMain.java | 115 ++++++++++++++++++ .../HadoopMRLoadVariantStoragePipeline.java | 23 +--- .../variant/executors/MRExecutorFactory.java | 5 +- 4 files changed, 159 insertions(+), 32 deletions(-) diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/app/AbstractMain.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/app/AbstractMain.java index 7c51704a1a8..91d9b6f2388 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/app/AbstractMain.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/app/AbstractMain.java @@ -122,24 +122,52 @@ protected static ObjectMap getArgsMap(String[] args, int firstIdx, String... key ObjectMap argsMap; argsMap = new ObjectMap(); int i = firstIdx; + int offset; while (i < args.length) { - String key = args[i]; - while (key.startsWith("-")) { - key = key.substring(1); + String inputKey = args[i]; + offset = 1; + String key; + String value; + if (inputKey.startsWith("--")) { + key = inputKey.substring(2); + value = safeArg(args, i + 1); + offset++; // one extra value read + } else if (inputKey.startsWith("-")) { + key = inputKey.substring(1, 2); + value = inputKey.substring(2); + if (value.isEmpty()) { + value = safeArg(args, i + 1); + offset++; // one extra value read + } + } else { + throw new IllegalArgumentException("Unknown argument '" + inputKey + "'"); + } + if (value == null || value.startsWith("-")) { + value = "true"; + offset--; // extra value discarded } if (!acceptedKeys.isEmpty()) { if (!acceptedKeys.contains(key)) { - throw new IllegalArgumentException("Unknown argument '" + args[i] + "'"); + throw new IllegalArgumentException("Unknown argument '" + inputKey + "'"); } } - String value = safeArg(args, i + 1); - if (value == null || value.startsWith("-")) { - argsMap.put(key, true); - i += 1; + + if (key.equals("D")) { + ObjectMap dynamic = (ObjectMap) argsMap.computeIfAbsent(key, k -> new ObjectMap()); + String[] split = value.split("=", 2); + if (split.length != 2) { + throw new IllegalArgumentException("Expected '-D key=value'"); + } + if (dynamic.put(split[0], split[1]) != null) { + throw new IllegalArgumentException("Duplicated argument '-D " + value + "'"); + } } else { - argsMap.put(key, value); - i += 2; + if (argsMap.put(key, value) != null) { + throw new IllegalArgumentException("Duplicated param '" + inputKey + "'"); + } } + i += offset; + } return argsMap; } diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/app/HBaseMain.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/app/HBaseMain.java index 004f4f8e2ff..f713fbc2e9e 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/app/HBaseMain.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/app/HBaseMain.java @@ -10,14 +10,21 @@ import org.apache.hadoop.hbase.client.SnapshotDescription; import org.apache.hadoop.hbase.client.TableState; import org.apache.hadoop.hbase.exceptions.IllegalArgumentIOException; +import org.apache.tools.ant.types.Commandline; import org.opencb.commons.ProgressLogger; import org.opencb.commons.datastore.core.ObjectMap; import org.opencb.opencga.core.common.TimeUtils; +import org.opencb.opencga.core.config.storage.StorageConfiguration; import org.opencb.opencga.storage.hadoop.utils.HBaseManager; +import org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngine; +import org.opencb.opencga.storage.hadoop.variant.executors.MRExecutor; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import java.io.FileInputStream; import java.io.IOException; +import java.nio.file.Path; +import java.nio.file.Paths; import java.time.Instant; import java.util.*; import java.util.stream.Collectors; @@ -36,6 +43,8 @@ public class HBaseMain extends AbstractMain { public static final String SNAPSHOT_TABLE = "snapshot-table"; public static final String DELETE_SNAPSHOTS = "delete-snapshots"; public static final String CLONE_SNAPSHOTS = "clone-snapshots"; + public static final String EXPORT_SNAPSHOTS = "export-snapshots"; + public static final String EXEC = "exec"; public static final String DISABLE_TABLE = "disable-table"; public static final String DROP_TABLE = "drop-table"; public static final String ENABLE_TABLE = "enable-table"; @@ -137,6 +146,25 @@ public void run(String[] args) throws Exception { ); break; } + case EXPORT_SNAPSHOTS: { + ObjectMap argsMap = getArgsMap(args, 1, "dryRun", "snapshot", "copy-to", "copy-to-local", "copy-from", "target", + "mappers", "overwrite", "D"); + exportSnapshot(null, + argsMap.getString("snapshot"), + argsMap.getString("copy-to"), + argsMap.getBoolean("copy-to-local"), + argsMap.getString("copy-from"), + argsMap.getString("target"), + argsMap.getString("mappers"), + argsMap.getBoolean("overwrite"), + argsMap.getBoolean("dryRun"), + argsMap); + break; + } + case EXEC: { + exec(getArg(args, 1), Arrays.asList(args).subList(2, args.length)); + break; + } case DISABLE_TABLE: { ObjectMap argsMap = getArgsMap(args, 2, "dryRun"); disableTables(getArg(args, 1), argsMap.getBoolean("dryRun")); @@ -186,6 +214,25 @@ public void run(String[] args) throws Exception { + "[--onExistingTables [fail|skip|drop] ]"); System.out.println(" Clone all snapshots into tables matching the regex. " + "Generated tables can have a table prefix change."); +// System.out.println(" " + EXPORT_SNAPSHOTS + " \n" +// + " --dryRun Dry run.\n" +// + " --snapshot Snapshot to restore.\n" +// + " --copyTo Remote destination hdfs://\n" +// + " --copyFrom Input folder hdfs:// (default hbase.rootdir)\n" +// + " --target Target name for the snapshot.\n" +//// + " --no-checksum-verify Do not verify checksum, use name+length only.\n" +//// + " --no-target-verify Do not verify the integrity of the exported snapshot.\n" +// + " --overwrite Rewrite the snapshot manifest if already exists.\n" +//// + " --chuser Change the owner of the files to the specified one.\n" +//// + " --chgroup Change the group of the files to the specified one.\n" +//// + " --chmod Change the permission of the files to the specified one.\n" +//// + " --bandwidth Limit bandwidth to this value in MB/second.\n" +// + " --mappers Number of mappers to use during the copy (mapreduce.job.maps).\n" +// + " -Dkey=value Other key-value fields"); +// System.out.println(" Clone all snapshots into tables matching the regex. " +// + "Generated tables can have a table prefix change."); + System.out.println(" " + EXEC + "[hadoop|yarn|hbase|hdfs]"); + System.out.println(" Execute a MR job on the hadoop cluster. Use \"exec yarn jar ....\""); System.out.println(" " + DISABLE_TABLE + " [--dryRun]"); System.out.println(" Disable all tables matching the regex."); System.out.println(" " + DROP_TABLE + " [--dryRun]"); @@ -199,6 +246,74 @@ public void run(String[] args) throws Exception { } + private void exec(String tool, List args) throws Exception { + Path opencgaHome = Paths.get(System.getProperty("app.home")); + String storageConfigurationPath = opencgaHome.resolve("conf").resolve("storage-configuration.yml").toString(); + StorageConfiguration storageConfiguration; + try (FileInputStream is = new FileInputStream(storageConfigurationPath)) { + storageConfiguration = StorageConfiguration.load(is); + } + + HadoopVariantStorageEngine engine = new HadoopVariantStorageEngine(); + engine.setConfiguration(storageConfiguration, HadoopVariantStorageEngine.STORAGE_ENGINE_ID, ""); + + MRExecutor mrExecutor = engine.getMRExecutor(); + mrExecutor.run(tool, args.toArray(new String[0])); + } + + private void exportSnapshot(String storageConfigurationPath, String snapshot, String copyTo, boolean copyToLocal, + String copyFrom, String target, + String mappers, boolean overwrite, boolean dryRun, ObjectMap options) throws Exception { + if (storageConfigurationPath == null) { + Path opencgaHome = Paths.get(System.getProperty("app.home")); + storageConfigurationPath = opencgaHome.resolve("conf").resolve("storage-configuration.yml").toString(); + } + StorageConfiguration storageConfiguration; + try (FileInputStream is = new FileInputStream(storageConfigurationPath)) { + storageConfiguration = StorageConfiguration.load(is); + } + + List args = new LinkedList<>(); + args.add(org.apache.hadoop.hbase.snapshot.ExportSnapshot.class.getName()); + for (Map.Entry entry : options.get("D", ObjectMap.class, new ObjectMap()).entrySet()) { + args.add("-D" + entry.getKey() + "=" + entry.getValue().toString()); + } + args.add("--snapshot"); + args.add(snapshot); + if (StringUtils.isNotEmpty(copyTo)) { + args.add("--copy-to"); + args.add(copyTo); + } else if (copyToLocal) { + args.add("--copy-to"); + args.add(hBaseManager.getConf().get(HConstants.HBASE_DIR)); + } + if (StringUtils.isNotEmpty(copyFrom)) { + args.add("--copy-from"); + args.add(copyFrom); + } + if (StringUtils.isNotEmpty(target)) { + args.add("--target"); + args.add(target); + } + if (overwrite) { + args.add("--overwrite"); + } + if (StringUtils.isNotEmpty(mappers)) { + args.add("--mappers"); + args.add(mappers); + } + + if (dryRun) { + System.out.println("hbase " + Commandline.toString(args.toArray(new String[0]))); + } else { + HadoopVariantStorageEngine engine = new HadoopVariantStorageEngine(); + engine.setConfiguration(storageConfiguration, HadoopVariantStorageEngine.STORAGE_ENGINE_ID, ""); + + MRExecutor mrExecutor = engine.getMRExecutor(); + mrExecutor.run("hbase", args.toArray(new String[0])); + } + } + private void regionsPerTable(String tableNameStr) throws Exception { // TableName tableName = getTable(tableNameStr); // hBaseManager.act(tableName.getNameAsString(), (table, admin) -> { diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/HadoopMRLoadVariantStoragePipeline.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/HadoopMRLoadVariantStoragePipeline.java index 06284118162..c508f42e848 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/HadoopMRLoadVariantStoragePipeline.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/HadoopMRLoadVariantStoragePipeline.java @@ -35,7 +35,6 @@ import java.io.IOException; import java.net.URI; -import static org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageOptions.MR_HADOOP_BIN; import static org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageOptions.INTERMEDIATE_HDFS_DIRECTORY; /** @@ -96,29 +95,11 @@ public URI preLoad(URI input, URI output) throws StorageEngineException { protected void load(URI input, URI outdir, int studyId, int fileId) throws StorageEngineException { URI vcfMeta = URI.create(VariantReaderUtils.getMetaFromTransformedFile(input.toString())); - - String hadoopRoute = options.getString(MR_HADOOP_BIN.key(), MR_HADOOP_BIN.defaultValue()); - String jar = MRExecutor.getJarWithDependencies(getOptions()); - - Class execClass = ArchiveDriver.class; - String executable = hadoopRoute + " jar " + jar + " " + execClass.getName(); String args = ArchiveDriver.buildCommandLineArgs(input, vcfMeta, dbAdaptor.getVariantTable(), getArchiveTable(), studyId, fileId, options); - - long startTime = System.currentTimeMillis(); - logger.info("------------------------------------------------------"); - logger.info("Loading file {} into archive table '{}'", fileId, getArchiveTable()); - logger.debug(executable + " " + args); - logger.info("------------------------------------------------------"); - int exitValue = mrExecutor.run(executable, Commandline.translateCommandline(args)); - logger.info("------------------------------------------------------"); - logger.info("Exit value: {}", exitValue); - logger.info("Total time: {}s", (System.currentTimeMillis() - startTime) / 1000.0); - if (exitValue != 0) { - throw new StorageEngineException("Error loading file " + input + " into archive table \"" - + getArchiveTable() + "\""); - } + mrExecutor.run(ArchiveDriver.class, Commandline.translateCommandline(args), + "Loading file " + fileId + " into archive table '" + getArchiveTable() + "'"); } } diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/executors/MRExecutorFactory.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/executors/MRExecutorFactory.java index 14325ec42ed..29666831779 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/executors/MRExecutorFactory.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/variant/executors/MRExecutorFactory.java @@ -10,7 +10,10 @@ * * @author Jacobo Coll <jacobo167@gmail.com> */ -public class MRExecutorFactory { +public final class MRExecutorFactory { + + private MRExecutorFactory() { + } public static MRExecutor getMRExecutor(ObjectMap options) throws StorageEngineException { MRExecutor mrExecutor; From 0d335223287137bb4b9d3306076c024287a40b04 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 12 Jul 2023 17:26:13 +0200 Subject: [PATCH 071/109] Fix needs in release.yml --- .github/workflows/release.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 0ed6340be1f..204f13d2b72 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -14,21 +14,21 @@ jobs: deploy-maven: uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop - needs: test + needs: build with: maven_opts: -P storage-hadoop,hdp3.1 -Dopencga.war.name=opencga secrets: inherit deploy-docker: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop - needs: test + needs: build with: cli: python3 ./build/cloud/docker/docker-build.py push --images base,init secrets: inherit deploy-python: uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop - needs: test + needs: build with: cli: ./clients/python/python-build.sh push artifact: build-folder From 95ed1adf2d269b4715def60d0c3d3826093d04a4 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 13 Jul 2023 08:39:35 +0200 Subject: [PATCH 072/109] update version --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-deps-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp2.6/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 2 +- 21 files changed, 21 insertions(+), 21 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index ec07e770980..ddefa7d2618 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.2.1 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 487f8a79b70..c0bc97362b9 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.2.1 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index a477a10338c..c911504528d 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 2.8.2.1 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 2253ab703c1..25c7042ce63 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.2.1 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 1f4081610ce..d7c383eec63 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 2.8.2.1 + 2.10.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 2d20981f882..b23641a3dbd 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.2.1 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index f1328ae8014..d1e079cf6a8 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 2.8.2.1 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index f31a834b58c..f16e51062b9 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.2.1 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index c880ba80e4d..209b780bb8c 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.8.2.1 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 1ffa40499d6..e43034af54f 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 2.8.2.1 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index e3680f726a9..95c37c68a8c 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -25,7 +25,7 @@ org.opencb.opencga opencga-storage - 2.8.2.1 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 4952d05abfa..ca90d6fc622 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.8.2.1 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml index ffa0a154cd5..001205ea43e 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.8.2.1 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml index 1e5cc5980ab..e8ed3f367fc 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.8.2.1 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml index 44eb9fb37a9..19403f3054e 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.8.2.1 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml index b3d21b69d62..f46f425eede 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml @@ -50,7 +50,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.8.2.1 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 44c89fd9b22..d2c588dc56f 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -28,7 +28,7 @@ org.opencb.opencga opencga-storage - 2.8.2.1 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 3a7acd6082b..42703d7ee32 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.8.2.1 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 21edba58336..643cebae481 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.2.1 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 6210dc8d2b0..18c878e910c 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 2.8.2.1 + 2.10.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index a71ba63f9d8..778d57c8df0 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.2.1 + 2.10.0-SNAPSHOT pom OpenCGA OenCGA projects implements a big data platform for genomic data analysis From 1319dca78325329eff09996d47169d24be609317 Mon Sep 17 00:00:00 2001 From: imedina Date: Mon, 17 Jul 2023 01:33:54 +0100 Subject: [PATCH 073/109] Prepare release 2.10.0 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-deps-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp2.6/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 21 files changed, 27 insertions(+), 27 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index ddefa7d2618..7844c61c782 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.10.0-SNAPSHOT + 2.10.0 ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index c0bc97362b9..b25eb3d7e06 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.10.0-SNAPSHOT + 2.10.0 ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index c911504528d..3e041c2a767 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 2.10.0-SNAPSHOT + 2.10.0 ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 25c7042ce63..9ae20b273bf 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.10.0-SNAPSHOT + 2.10.0 ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index d7c383eec63..2b909b97d2c 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 2.10.0-SNAPSHOT + 2.10.0 ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index b23641a3dbd..52e0d9d9795 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.10.0-SNAPSHOT + 2.10.0 ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index d1e079cf6a8..14e9ff88442 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 2.10.0-SNAPSHOT + 2.10.0 ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index f16e51062b9..229956a4b60 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.10.0-SNAPSHOT + 2.10.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 209b780bb8c..9c06003c1e6 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.10.0-SNAPSHOT + 2.10.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index e43034af54f..08a6603cd59 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 2.10.0-SNAPSHOT + 2.10.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 95c37c68a8c..85c6321289e 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -25,7 +25,7 @@ org.opencb.opencga opencga-storage - 2.10.0-SNAPSHOT + 2.10.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index ca90d6fc622..ee34b8f5284 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.10.0-SNAPSHOT + 2.10.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml index 001205ea43e..30c0ceba8df 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.10.0-SNAPSHOT + 2.10.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml index e8ed3f367fc..d9705a34f36 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.10.0-SNAPSHOT + 2.10.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml index 19403f3054e..6dcbbea5635 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.10.0-SNAPSHOT + 2.10.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml index f46f425eede..7c5d8e9cc86 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml @@ -50,7 +50,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.10.0-SNAPSHOT + 2.10.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index d2c588dc56f..39134f16293 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -28,7 +28,7 @@ org.opencb.opencga opencga-storage - 2.10.0-SNAPSHOT + 2.10.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 42703d7ee32..ee14da290e4 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.10.0-SNAPSHOT + 2.10.0 ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 643cebae481..288064b9406 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.10.0-SNAPSHOT + 2.10.0 ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 18c878e910c..a34e79d3d87 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 2.10.0-SNAPSHOT + 2.10.0 ../pom.xml diff --git a/pom.xml b/pom.xml index 4d35b06f169..7469f82817d 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.10.0-SNAPSHOT + 2.10.0 pom OpenCGA OpenCGA projects implements a big data platform for genomic data analysis @@ -42,12 +42,12 @@ - 2.10.0_dev - 2.10.0_dev - 5.6.0-SNAPSHOT - 2.10.0-SNAPSHOT - 4.10.0-SNAPSHOT - 2.10.0-SNAPSHOT + 2.10.0 + 2.10.0 + 5.6.0 + 2.10.0 + 4.10.0 + 2.10.0 0.2.0 From a19ea40fb4c466b86df0a2b5714ffbe00b2173cb Mon Sep 17 00:00:00 2001 From: imedina Date: Mon, 17 Jul 2023 01:37:14 +0100 Subject: [PATCH 074/109] Prepare new development branch release-2.10.x --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-deps-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp2.6/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 21 files changed, 27 insertions(+), 27 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 7844c61c782..adcb53e2d0e 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.10.0 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index b25eb3d7e06..b787e5d11d2 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.10.0 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 3e041c2a767..fac7d8e548a 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 2.10.0 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 9ae20b273bf..22a563296b0 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.10.0 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 2b909b97d2c..de52a8ef4e1 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 2.10.0 + 2.11.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 52e0d9d9795..e2d8fc127e4 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.10.0 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 14e9ff88442..2d6fd5a8da6 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 2.10.0 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 229956a4b60..65cebaebdda 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.10.0 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 9c06003c1e6..cafb6d1c2ac 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.10.0 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 08a6603cd59..aa79ec720fd 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 2.10.0 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 85c6321289e..b97d0472984 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -25,7 +25,7 @@ org.opencb.opencga opencga-storage - 2.10.0 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index ee34b8f5284..97db69b63b9 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.10.0 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml index 30c0ceba8df..1c27bd10350 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.10.0 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml index d9705a34f36..f1f99b70468 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.10.0 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml index 6dcbbea5635..03561e6c93d 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.10.0 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml index 7c5d8e9cc86..c0e60a63db5 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml @@ -50,7 +50,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.10.0 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 39134f16293..1ea5e5a91d1 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -28,7 +28,7 @@ org.opencb.opencga opencga-storage - 2.10.0 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index ee14da290e4..c9a6b5604a3 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.10.0 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 288064b9406..49b680170d0 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.10.0 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index a34e79d3d87..caa613c03e2 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 2.10.0 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 7469f82817d..c0b9f02fd71 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.10.0 + 2.11.0-SNAPSHOT pom OpenCGA OpenCGA projects implements a big data platform for genomic data analysis @@ -42,12 +42,12 @@ - 2.10.0 - 2.10.0 - 5.6.0 - 2.10.0 - 4.10.0 - 2.10.0 + 2.11.0_dev + 2.11.0_dev + 5.7.0-SNAPSHOT + 2.11.0-SNAPSHOT + 4.11.0-SNAPSHOT + 2.11.0-SNAPSHOT 0.2.0 From 7d4ed6df4477d6e063fb5ef1c5b19de642c04122 Mon Sep 17 00:00:00 2001 From: imedina Date: Mon, 17 Jul 2023 01:41:02 +0100 Subject: [PATCH 075/109] cicd: fix develop.yml 'needs' variable --- .github/workflows/develop.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml index 0e8f622a2b6..50c396dd7cc 100644 --- a/.github/workflows/develop.yml +++ b/.github/workflows/develop.yml @@ -15,7 +15,7 @@ jobs: test: uses: ./.github/workflows/test-analysis.yml - needs: deploy-docker-ext-tools + needs: build with: test_profile: runShortTests,runMediumTests secrets: inherit From e65f12950761b888173be62446b167bb76ba6184 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 21 Jul 2023 13:56:50 +0200 Subject: [PATCH 076/109] Fix weekend cicd syntax --- .github/workflows/long-test-analysis.yml | 4 ++-- .../storage/core/variant/annotation/DummyTestAnnotator.java | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/long-test-analysis.yml b/.github/workflows/long-test-analysis.yml index ef610d74bda..c898c4dfa0b 100644 --- a/.github/workflows/long-test-analysis.yml +++ b/.github/workflows/long-test-analysis.yml @@ -5,13 +5,13 @@ name: Long test for run only on weekend on: schedule: - cron: '10 1 * * 6' + workflow_dispatch: jobs: test: uses: ./.github/workflows/test-analysis.yml secrets: inherit with: - test_profile: runLongTests,runMediumTests,runShortTests - report_context: development + test_profile: runShortTests,runMediumTests,runLongTests, diff --git a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/DummyTestAnnotator.java b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/DummyTestAnnotator.java index 71f5135e08c..b36e8fa90ad 100644 --- a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/DummyTestAnnotator.java +++ b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/DummyTestAnnotator.java @@ -59,7 +59,7 @@ public List annotate(List variants) throws VariantAn public ProjectMetadata.VariantAnnotationMetadata getVariantAnnotationMetadata() throws VariantAnnotatorException { return new ProjectMetadata.VariantAnnotationMetadata(-1, null, null, new ProjectMetadata.VariantAnnotatorProgram("MyAnnotator", key, null), - Collections.singletonList(new ObjectMap("data", "genes")), null); + Collections.singletonList(new ObjectMap("data", "genes")), null,null); } } From 026500f25a9c59c1bac60d1be8f1912e0d319ebc Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 24 Jul 2023 10:28:23 +0200 Subject: [PATCH 077/109] Prepare release 2.9.2 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-deps-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp2.6/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 21 files changed, 27 insertions(+), 27 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index aec5669b12f..90785305aeb 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.2-SNAPSHOT + 2.9.2 ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index a9fe3703f97..487a5db6a10 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.2-SNAPSHOT + 2.9.2 ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 43fb05be14d..72f6826b01c 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 2.9.2-SNAPSHOT + 2.9.2 ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index bed3ac24829..0fe70424e93 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.2-SNAPSHOT + 2.9.2 ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 9f85a0ff7d0..4c2ca0fcc8f 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 2.9.2-SNAPSHOT + 2.9.2 ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 8544e3bbd09..169f823dc73 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.2-SNAPSHOT + 2.9.2 ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 898205375bc..588edea3bec 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 2.9.2-SNAPSHOT + 2.9.2 ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 957eb127745..ce486179b63 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.2-SNAPSHOT + 2.9.2 ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 45bd1dd22c1..c8b4d7baaab 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.9.2-SNAPSHOT + 2.9.2 ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index cdd5e80590b..529f72d4704 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 2.9.2-SNAPSHOT + 2.9.2 ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index ab277249b74..2fb5ee548ad 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -25,7 +25,7 @@ org.opencb.opencga opencga-storage - 2.9.2-SNAPSHOT + 2.9.2 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 2ef22a0bf03..8e77648c007 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.9.2-SNAPSHOT + 2.9.2 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml index 6ed975a82d8..1184125129d 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.9.2-SNAPSHOT + 2.9.2 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml index 422fa4f30c2..e0433aecf75 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.9.2-SNAPSHOT + 2.9.2 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml index a2e8db3647b..6dfda56b33c 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.9.2-SNAPSHOT + 2.9.2 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml index 246bdd0cc61..2a11460e046 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml @@ -50,7 +50,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.9.2-SNAPSHOT + 2.9.2 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index e7302b47a65..1e3a6fe0ab7 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -28,7 +28,7 @@ org.opencb.opencga opencga-storage - 2.9.2-SNAPSHOT + 2.9.2 ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 580e03d7ebc..6ada960d62c 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.9.2-SNAPSHOT + 2.9.2 ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index eff64556c36..5147b9ca3db 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.2-SNAPSHOT + 2.9.2 ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 6b0e2013c39..83b52baf0c0 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 2.9.2-SNAPSHOT + 2.9.2 ../pom.xml diff --git a/pom.xml b/pom.xml index f36ef9ca58a..76c206990bb 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.2-SNAPSHOT + 2.9.2 pom OpenCGA OenCGA projects implements a big data platform for genomic data analysis @@ -42,12 +42,12 @@ - 2.9.2_dev - 2.9.2_dev - 5.5.1-SNAPSHOT - 2.9.1-SNAPSHOT - 4.9.1-SNAPSHOT - 2.9.2-SNAPSHOT + 2.9.2 + 2.9.2 + 5.5.0 + 2.9.0 + 4.9.0 + 2.9.2 0.2.0 2.11.4 From 0531651b3809695c77c6526e4fb7053e9e23de8b Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 25 Jul 2023 10:17:51 +0200 Subject: [PATCH 078/109] Update version for Port Patch 1.7.2 -> 1.9.0 #TASK-4810 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-deps-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp2.6/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 2 +- 21 files changed, 21 insertions(+), 21 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 90785305aeb..adcb53e2d0e 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.2 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 487a5db6a10..b787e5d11d2 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.2 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 72f6826b01c..fac7d8e548a 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 2.9.2 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 0fe70424e93..22a563296b0 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.2 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 4c2ca0fcc8f..de52a8ef4e1 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 2.9.2 + 2.11.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 169f823dc73..e2d8fc127e4 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.2 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 588edea3bec..2d6fd5a8da6 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 2.9.2 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index ce486179b63..65cebaebdda 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.2 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index c8b4d7baaab..cafb6d1c2ac 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.9.2 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 529f72d4704..aa79ec720fd 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 2.9.2 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 2fb5ee548ad..b97d0472984 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -25,7 +25,7 @@ org.opencb.opencga opencga-storage - 2.9.2 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 8e77648c007..97db69b63b9 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.9.2 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml index 1184125129d..1c27bd10350 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.9.2 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml index e0433aecf75..f1f99b70468 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.9.2 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml index 6dfda56b33c..03561e6c93d 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.9.2 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml index 2a11460e046..c0e60a63db5 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml @@ -50,7 +50,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.9.2 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 1e3a6fe0ab7..1ea5e5a91d1 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -28,7 +28,7 @@ org.opencb.opencga opencga-storage - 2.9.2 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 6ada960d62c..c9a6b5604a3 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.9.2 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 5147b9ca3db..49b680170d0 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.2 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 83b52baf0c0..caa613c03e2 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 2.9.2 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 76c206990bb..061edc3cead 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.9.2 + 2.11.0-SNAPSHOT pom OpenCGA OenCGA projects implements a big data platform for genomic data analysis From cd665a651e6395b4714faf75fab96900ca445bec Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 26 Jul 2023 10:53:02 +0200 Subject: [PATCH 079/109] CICD: docker-ext tools deploy workflow --- .github/workflows/docker-ext-tools.yml | 48 +++++++++++++++++++++----- 1 file changed, 39 insertions(+), 9 deletions(-) diff --git a/.github/workflows/docker-ext-tools.yml b/.github/workflows/docker-ext-tools.yml index 07062f03278..8241c3c5d66 100644 --- a/.github/workflows/docker-ext-tools.yml +++ b/.github/workflows/docker-ext-tools.yml @@ -1,18 +1,48 @@ name: Deploy Docker Ext-Tools - on: - push: - branches: - - develop - - release-* - - TASK-* - paths: - - opencga-app/app/cloud/docker/opencga-ext-tools/Dockerfile workflow_dispatch: + inputs: + ref: + description: "The branch, tag or SHA to build docker. Otherwise, uses develop branch." + type: string + required: false + default: "" jobs: build: - uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop + name: Build Java app + runs-on: ubuntu-22.04 + outputs: + version: ${{ steps.get_project_version.outputs.version }} + steps: + - uses: actions/checkout@v3 + with: + fetch-depth: '10' + ref: "${{ inputs.ref }}" + - name: Set up JDK 8 + uses: actions/setup-java@v3 + with: + distribution: 'temurin' + java-version: '8' + cache: 'maven' + - name: Install dependencies branches + run: | + if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then + chmod +x ./.github/workflows/scripts/get_same_branch.sh + ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }} + fi + - name: Maven Build (skip tests) + run: mvn -T 2 clean install -DskipTests + - uses: actions/upload-artifact@v3 + with: + name: build-folder + path: build + - id: get_project_version + uses: avides/actions-project-version-check@v1.3.0 + with: + token: ${{ secrets.GITHUB_TOKEN }} + file-to-check: pom.xml + only-return-version: true deploy-docker-ext-tools: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop From 84c1e0d8f5cd1961c90e908b17a45774ad037ce6 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 26 Jul 2023 22:38:57 +0200 Subject: [PATCH 080/109] Docker ext-tools manual deployer yml --- .github/workflows/docker-ext-tools.yml | 52 ++++--------------- .github/workflows/manual-deploy-ext-tools.yml | 51 ++++++++++++++++++ 2 files changed, 61 insertions(+), 42 deletions(-) create mode 100644 .github/workflows/manual-deploy-ext-tools.yml diff --git a/.github/workflows/docker-ext-tools.yml b/.github/workflows/docker-ext-tools.yml index 8241c3c5d66..6ded6d96fbe 100644 --- a/.github/workflows/docker-ext-tools.yml +++ b/.github/workflows/docker-ext-tools.yml @@ -1,53 +1,21 @@ name: Deploy Docker Ext-Tools + on: - workflow_dispatch: - inputs: - ref: - description: "The branch, tag or SHA to build docker. Otherwise, uses develop branch." - type: string - required: false - default: "" + push: + branches: + - develop + - release-* + - TASK-* + paths: + - opencga-app/app/cloud/docker/opencga-ext-tools/Dockerfile jobs: build: - name: Build Java app - runs-on: ubuntu-22.04 - outputs: - version: ${{ steps.get_project_version.outputs.version }} - steps: - - uses: actions/checkout@v3 - with: - fetch-depth: '10' - ref: "${{ inputs.ref }}" - - name: Set up JDK 8 - uses: actions/setup-java@v3 - with: - distribution: 'temurin' - java-version: '8' - cache: 'maven' - - name: Install dependencies branches - run: | - if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then - chmod +x ./.github/workflows/scripts/get_same_branch.sh - ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }} - fi - - name: Maven Build (skip tests) - run: mvn -T 2 clean install -DskipTests - - uses: actions/upload-artifact@v3 - with: - name: build-folder - path: build - - id: get_project_version - uses: avides/actions-project-version-check@v1.3.0 - with: - token: ${{ secrets.GITHUB_TOKEN }} - file-to-check: pom.xml - only-return-version: true + uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop deploy-docker-ext-tools: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: build with: cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }} - secrets: inherit - + secrets: inherit \ No newline at end of file diff --git a/.github/workflows/manual-deploy-ext-tools.yml b/.github/workflows/manual-deploy-ext-tools.yml new file mode 100644 index 00000000000..7dbf4b5a104 --- /dev/null +++ b/.github/workflows/manual-deploy-ext-tools.yml @@ -0,0 +1,51 @@ +name: Deploy Docker Ext-Tools +on: + workflow_dispatch: + inputs: + branch: + description: "The branch, tag or SHA to build docker." + type: string + required: true + tag: + description: "The tag for the docker." + type: string + required: true + +jobs: + build: + name: Build Java app + runs-on: ubuntu-22.04 + outputs: + version: ${{ steps.get_project_version.outputs.version }} + steps: + - uses: actions/checkout@v3 + with: + fetch-depth: '10' + ref: "${{ inputs.branch }}" + - name: Set up JDK 8 + uses: actions/setup-java@v3 + with: + distribution: 'temurin' + java-version: '8' + cache: 'maven' + - name: Install dependencies branches + run: | + if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then + chmod +x ./.github/workflows/scripts/get_same_branch.sh + ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }} + fi + - name: Maven Build (skip tests) + run: mvn -T 2 clean install -DskipTests + - uses: actions/upload-artifact@v3 + with: + name: build-folder + path: build + + + deploy-docker-ext-tools: + uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop + needs: build + with: + cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ inputs.tag }} + secrets: inherit + From 6d427175ada253076f632efe214627ce21703a15 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 26 Jul 2023 22:42:28 +0200 Subject: [PATCH 081/109] Docker ext-tools manual deployer yml --- .github/workflows/manual-deploy-ext-tools.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/manual-deploy-ext-tools.yml b/.github/workflows/manual-deploy-ext-tools.yml index 7dbf4b5a104..eb8d2347137 100644 --- a/.github/workflows/manual-deploy-ext-tools.yml +++ b/.github/workflows/manual-deploy-ext-tools.yml @@ -3,11 +3,11 @@ on: workflow_dispatch: inputs: branch: - description: "The branch, tag or SHA to build docker." + description: "The branch, tag or SHA of the source code to build docker." type: string required: true tag: - description: "The tag for the docker." + description: "The tag for the new docker." type: string required: true From a995463a69c4179ac5ecfb46996e869fe2f8dd8d Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 26 Jul 2023 22:44:52 +0200 Subject: [PATCH 082/109] Docker ext-tools manual deployer yml --- .github/workflows/manual-deploy-ext-tools.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/manual-deploy-ext-tools.yml b/.github/workflows/manual-deploy-ext-tools.yml index eb8d2347137..3f64fd392de 100644 --- a/.github/workflows/manual-deploy-ext-tools.yml +++ b/.github/workflows/manual-deploy-ext-tools.yml @@ -1,4 +1,4 @@ -name: Deploy Docker Ext-Tools +name: Manual deploy Docker Ext-Tools on: workflow_dispatch: inputs: @@ -47,5 +47,4 @@ jobs: needs: build with: cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ inputs.tag }} - secrets: inherit - + secrets: inherit \ No newline at end of file From 13899a0062e067cb0f09bcd5c1e0c902a00f8c13 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 9 Aug 2023 15:54:04 +0200 Subject: [PATCH 083/109] Manual docker generate --- .github/workflows/manual-deploy-docker.yml | 50 ++++++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 .github/workflows/manual-deploy-docker.yml diff --git a/.github/workflows/manual-deploy-docker.yml b/.github/workflows/manual-deploy-docker.yml new file mode 100644 index 00000000000..a22f4dd4563 --- /dev/null +++ b/.github/workflows/manual-deploy-docker.yml @@ -0,0 +1,50 @@ +name: Manual deploy Docker base +on: + workflow_dispatch: + inputs: + branch: + description: "The branch, tag or SHA of the source code to build docker." + type: string + required: true + tag: + description: "The tag for the new docker." + type: string + required: true + +jobs: + build: + name: Build Java app + runs-on: ubuntu-22.04 + outputs: + version: ${{ steps.get_project_version.outputs.version }} + steps: + - uses: actions/checkout@v3 + with: + fetch-depth: '10' + ref: "${{ inputs.branch }}" + - name: Set up JDK 8 + uses: actions/setup-java@v3 + with: + distribution: 'temurin' + java-version: '8' + cache: 'maven' + - name: Install dependencies branches + run: | + if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then + chmod +x ./.github/workflows/scripts/get_same_branch.sh + ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }} + fi + - name: Maven Build (skip tests) + run: mvn -T 2 clean install -DskipTests + - uses: actions/upload-artifact@v3 + with: + name: build-folder + path: build + + + deploy-docker-ext-tools: + uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop + needs: build + with: + cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ inputs.tag }} + secrets: inherit \ No newline at end of file From 3e42c2e7e0787c3a4c1617789f7c9b897601c0a8 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Thu, 10 Aug 2023 13:37:33 +0200 Subject: [PATCH 084/109] rename step deploy-docker --- .github/workflows/manual-deploy-docker.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/manual-deploy-docker.yml b/.github/workflows/manual-deploy-docker.yml index a22f4dd4563..3c9660bbb2c 100644 --- a/.github/workflows/manual-deploy-docker.yml +++ b/.github/workflows/manual-deploy-docker.yml @@ -42,7 +42,7 @@ jobs: path: build - deploy-docker-ext-tools: + deploy-docker: uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop needs: build with: From 3213ffeb3966d03f35eac210caa469a4fc806fb9 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Fri, 11 Aug 2023 12:26:59 +0200 Subject: [PATCH 085/109] storage-core: Added ANNOTATION_PHARMACOGENOMICS to VariantField.java #TASK-4848 --- .../opencga/storage/core/variant/adaptors/VariantField.java | 1 + 1 file changed, 1 insertion(+) diff --git a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/adaptors/VariantField.java b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/adaptors/VariantField.java index d0eb0a335e6..8c208b1cd30 100644 --- a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/adaptors/VariantField.java +++ b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/adaptors/VariantField.java @@ -71,6 +71,7 @@ public enum VariantField { ANNOTATION_CONSERVATION(ANNOTATION, "annotation.conservation"), ANNOTATION_CANCER_HOTSPOTS(ANNOTATION, "annotation.cancerHotspots"), ANNOTATION_GENE_EXPRESSION(ANNOTATION, "annotation.geneExpression"), + ANNOTATION_PHARMACOGENOMICS(ANNOTATION, "annotation.pharmacogenomics"), ANNOTATION_GENE_TRAIT_ASSOCIATION(ANNOTATION, "annotation.geneTraitAssociation"), ANNOTATION_GENE_DRUG_INTERACTION(ANNOTATION, "annotation.geneDrugInteraction"), ANNOTATION_GENE_CANCER_ASSOCIATIONS(ANNOTATION, "annotation.geneCancerAssociations"), From aed710fdd2ab13f3bd4d81754717133689a547bb Mon Sep 17 00:00:00 2001 From: pfurio Date: Mon, 28 Aug 2023 10:52:08 +0200 Subject: [PATCH 086/109] core: add REGEX comment to /search and /distinct, #TASK-4248 --- .../opencga/core/api/ParamConstants.java | 65 ++++++++++--------- 1 file changed, 33 insertions(+), 32 deletions(-) diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java b/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java index b65214a9ba4..6a42182cf34 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java @@ -38,6 +38,7 @@ public class ParamConstants { public static final String RELEASE_DESCRIPTION = "Release when it was created"; public static final String INTERNAL_STATUS_PARAM = "internalStatus"; public static final String INTERNAL_STATUS_DESCRIPTION = "Filter by internal status"; + private static final String REGEX_SUPPORT = ". Also admits basic regular expressions like '~/^value/i'"; @Deprecated // Use INTERNAL_VARIANT_INDEX_STATUS_PARAM public static final String INTERNAL_INDEX_STATUS_PARAM = "internalIndexStatus"; public static final String INTERNAL_VARIANT_INDEX_STATUS_PARAM = "internalVariantIndexStatus"; @@ -169,12 +170,12 @@ public class ParamConstants { + "exception whenever one of the entries looked for cannot be shown for whichever reason"; public static final String FILE_ID_DESCRIPTION = "File ID"; public static final String FILE_NAME_DESCRIPTION = "File name"; - public static final String FILE_NAMES_DESCRIPTION = "Comma separated list of file names"; + public static final String FILE_NAMES_DESCRIPTION = "Comma separated list of file names" + REGEX_SUPPORT; // --------------------------------------------- public static final String FILE_PATH_PARAM = "path"; public static final String FILE_PATH_DESCRIPTION = "File path"; - public static final String FILE_PATHS_DESCRIPTION = "Comma separated list of paths"; - public static final String FILE_URIS_DESCRIPTION = "Comma separated list of uris"; + public static final String FILE_PATHS_DESCRIPTION = "Comma separated list of paths" + REGEX_SUPPORT; + public static final String FILE_URIS_DESCRIPTION = "Comma separated list of uris" + REGEX_SUPPORT; public static final String FILE_TYPE_DESCRIPTION = "File type, either FILE or DIRECTORY"; public static final String FILE_FORMAT_DESCRIPTION = "Comma separated Format values. For existing Formats see files/formats"; public static final String FILE_EXTERNAL_DESCRIPTION = "Boolean field indicating whether to filter by external or non external files"; @@ -182,7 +183,7 @@ public class ParamConstants { "files/bioformats"; public static final String FILE_STATUS_DESCRIPTION = "File status"; public static final String FILE_DESCRIPTION_DESCRIPTION = "Description"; - public static final String FILE_TAGS_DESCRIPTION = "Tags"; + public static final String FILE_TAGS_DESCRIPTION = "Tags" + REGEX_SUPPORT; public static final String FILE_SOFTWARE_NAME_PARAM = "softwareName"; public static final String FILE_SOFTWARE_NAME_DESCRIPTION = "Software name"; public static final String FILE_JOB_ID_DESCRIPTION = "Job ID that created the file(s) or folder(s)"; @@ -316,12 +317,12 @@ public class ParamConstants { public static final String INDIVIDUAL_MOTHER_DESCRIPTION = "Mother ID, name or UUID"; public static final String INDIVIDUAL_SAMPLES_DESCRIPTION = "Sample ID, name or UUID"; public static final String INDIVIDUAL_SEX_DESCRIPTION = "Individual sex"; - public static final String INDIVIDUAL_ETHNICITY_DESCRIPTION = "Individual ethnicity"; + public static final String INDIVIDUAL_ETHNICITY_DESCRIPTION = "Individual ethnicity" + REGEX_SUPPORT; public static final String INDIVIDUAL_DATE_OF_BIRTH_DESCRIPTION = "Individual date of birth"; - public static final String INDIVIDUAL_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION; - public static final String INDIVIDUAL_PHENOTYPES_DESCRIPTION = PHENOTYPES_DESCRIPTION; - public static final String INDIVIDUAL_POPULATION_NAME_DESCRIPTION = "Population name"; - public static final String INDIVIDUAL_POPULATION_SUBPOPULATION_DESCRIPTION = "Subpopulation name"; + public static final String INDIVIDUAL_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION + REGEX_SUPPORT; + public static final String INDIVIDUAL_PHENOTYPES_DESCRIPTION = PHENOTYPES_DESCRIPTION + REGEX_SUPPORT; + public static final String INDIVIDUAL_POPULATION_NAME_DESCRIPTION = "Population name" + REGEX_SUPPORT; + public static final String INDIVIDUAL_POPULATION_SUBPOPULATION_DESCRIPTION = "Subpopulation name" + REGEX_SUPPORT; public static final String INDIVIDUAL_KARYOTYPIC_SEX_DESCRIPTION = "Individual karyotypic sex"; public static final String INDIVIDUAL_LIFE_STATUS_DESCRIPTION = "Individual life status"; public static final String INDIVIDUAL_DELETED_DESCRIPTION = DELETED_DESCRIPTION; @@ -358,8 +359,8 @@ public class ParamConstants { public static final String FAMILY_MEMBERS_DESCRIPTION = "Comma separated list of family members"; public static final String FAMILY_SAMPLES_DESCRIPTION = "Comma separated list of member's samples"; public static final String FAMILY_EXPECTED_SIZE_DESCRIPTION = "Expected size of the family (number of members)"; - public static final String FAMILY_PHENOTYPES_DESCRIPTION = PHENOTYPES_DESCRIPTION; - public static final String FAMILY_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION; + public static final String FAMILY_PHENOTYPES_DESCRIPTION = PHENOTYPES_DESCRIPTION + REGEX_SUPPORT; + public static final String FAMILY_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION + REGEX_SUPPORT; public static final String FAMILY_CREATION_DATE_DESCRIPTION = CREATION_DATE_DESCRIPTION; public static final String FAMILY_MODIFICATION_DATE_DESCRIPTION = MODIFICATION_DATE_DESCRIPTION; public static final String FAMILY_DELETED_DESCRIPTION = DELETED_DESCRIPTION; @@ -422,7 +423,7 @@ public class ParamConstants { public static final String CLINICAL_STATUS_PARAM = STATUS_PARAM; public static final String CLINICAL_INTERNAL_STATUS_PARAM = INTERNAL_STATUS_PARAM; public static final String CLINICAL_TYPE_DESCRIPTION = "Clinical Analysis type"; - public static final String CLINICAL_DISORDER_DESCRIPTION = "Clinical Analysis disorder"; + public static final String CLINICAL_DISORDER_DESCRIPTION = "Clinical Analysis disorder" + REGEX_SUPPORT; public static final String CLINICAL_FILES_DESCRIPTION = "Clinical Analysis files"; public static final String CLINICAL_SAMPLE_DESCRIPTION = "Sample associated to the proband or any member of a family"; public static final String CLINICAL_INDIVIDUAL_DESCRIPTION = "Proband or any member of a family"; @@ -466,7 +467,7 @@ public class ParamConstants { public static final String INTERPRETATION_LOCKED_PARAM = "locked"; public static final String INTERPRETATION_CLINICAL_ANALYSIS_ID_DESCRIPTION = "Clinical Analysis id"; public static final String INTERPRETATION_ANALYST_ID_DESCRIPTION = "Analyst ID"; - public static final String INTERPRETATION_METHOD_NAME_DESCRIPTION = "Interpretation method name"; + public static final String INTERPRETATION_METHOD_NAME_DESCRIPTION = "Interpretation method name" + REGEX_SUPPORT; public static final String INTERPRETATION_PANELS_DESCRIPTION = "Interpretation panels"; public static final String INTERPRETATION_PRIMARY_FINDINGS_IDS_DESCRIPTION = "Interpretation primary findings"; public static final String INTERPRETATION_SECONDARY_FINDINGS_IDS_DESCRIPTION = "Interpretation secondary findings"; @@ -498,12 +499,12 @@ public class ParamConstants { public static final String PANEL_ACL_PARAM = ACL_PARAM; public static final String PANEL_RELEASE_PARAM = RELEASE_PARAM; public static final String PANEL_SNAPSHOT_PARAM = SNAPSHOT_PARAM; - public static final String PANEL_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION; - public static final String PANEL_VARIANTS_DESCRIPTION = "Comma separated list of variant ids"; - public static final String PANEL_GENES_DESCRIPTION = "Comma separated list of gene ids"; - public static final String PANEL_REGIONS_DESCRIPTION = "Comma separated list of regions"; - public static final String PANEL_CATEGORIES_DESCRIPTION = "Comma separated list of category names"; - public static final String PANEL_TAGS_DESCRIPTION = "Panel tags"; + public static final String PANEL_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION + REGEX_SUPPORT; + public static final String PANEL_VARIANTS_DESCRIPTION = "Comma separated list of variant ids" + REGEX_SUPPORT; + public static final String PANEL_GENES_DESCRIPTION = "Comma separated list of gene ids" + REGEX_SUPPORT; + public static final String PANEL_REGIONS_DESCRIPTION = "Comma separated list of regions" + REGEX_SUPPORT; + public static final String PANEL_CATEGORIES_DESCRIPTION = "Comma separated list of category names" + REGEX_SUPPORT; + public static final String PANEL_TAGS_DESCRIPTION = "Panel tags" + REGEX_SUPPORT; public static final String PANEL_DELETED_DESCRIPTION = DELETED_DESCRIPTION; public static final String PANEL_STATUS_DESCRIPTION = STATUS_DESCRIPTION; @@ -539,7 +540,7 @@ public class ParamConstants { public static final String JOB_DEPENDS_ON_DESCRIPTION = "Comma separated list of existing job IDs the job will depend on."; public static final String JOB_TOOL_ID_PARAM = "toolId"; public static final String JOB_TOOL_TYPE_PARAM = "toolType"; - public static final String JOB_TOOL_ID_DESCRIPTION = "Tool ID executed by the job"; + public static final String JOB_TOOL_ID_DESCRIPTION = "Tool ID executed by the job" + REGEX_SUPPORT; public static final String JOB_TOOL_TYPE_DESCRIPTION = "Tool type executed by the job [OPERATION, ANALYSIS]"; public static final String JOB_USER_PARAM = "userId"; public static final String JOB_USER_DESCRIPTION = "User that created the job"; @@ -1475,34 +1476,34 @@ public class ParamConstants { public static final String ADMIN_CATALOG_JWT_SECRETKEY = "The body web service secretKey parameter"; private static final String UP_TO_100 = " up to a maximum of 100"; public static final String FILES_DESCRIPTION = "Comma separated list of file IDs or names" + UP_TO_100; - public static final String FILES_ID_DESCRIPTION = "Comma separated list of file IDs" + UP_TO_100; + public static final String FILES_ID_DESCRIPTION = "Comma separated list of file IDs" + UP_TO_100 + REGEX_SUPPORT; public static final String FILES_UUID_DESCRIPTION = "Comma separated list file UUIDs" + UP_TO_100; public static final String SAMPLES_DESCRIPTION = "Comma separated list sample IDs or UUIDs" + UP_TO_100; public static final String SAMPLES_ID_DESCRIPTION = "Comma separated list sample IDs" + UP_TO_100; public static final String SAMPLES_UUID_DESCRIPTION = "Comma separated list sample UUIDs" + UP_TO_100; public static final String INDIVIDUALS_DESCRIPTION = "Comma separated list of individual IDs, names or UUIDs" + UP_TO_100; - public static final String INDIVIDUALS_ID_DESCRIPTION = "Comma separated list individual IDs" + UP_TO_100; - public static final String INDIVIDUAL_NAME_DESCRIPTION = "Comma separated list individual names" + UP_TO_100; + public static final String INDIVIDUALS_ID_DESCRIPTION = "Comma separated list individual IDs" + UP_TO_100 + REGEX_SUPPORT; + public static final String INDIVIDUAL_NAME_DESCRIPTION = "Comma separated list individual names" + UP_TO_100 + REGEX_SUPPORT; public static final String INDIVIDUAL_UUID_DESCRIPTION = "Comma separated list individual UUIDs" + UP_TO_100; public static final String FAMILIES_DESCRIPTION = "Comma separated list of family IDs or names" + UP_TO_100; - public static final String FAMILY_ID_DESCRIPTION = "Comma separated list family IDs" + UP_TO_100; - public static final String FAMILY_NAME_DESCRIPTION = "Comma separated list family names" + UP_TO_100; + public static final String FAMILY_ID_DESCRIPTION = "Comma separated list family IDs" + UP_TO_100 + REGEX_SUPPORT; + public static final String FAMILY_NAME_DESCRIPTION = "Comma separated list family names" + UP_TO_100 + REGEX_SUPPORT; public static final String FAMILY_UUID_DESCRIPTION = "Comma separated list family UUIDs" + UP_TO_100; public static final String COHORTS_DESCRIPTION = "Comma separated list of cohort IDs or UUIDs" + UP_TO_100; - public static final String COHORT_IDS_DESCRIPTION = "Comma separated list of cohort IDs" + UP_TO_100; - public static final String COHORT_NAMES_DESCRIPTION = "Comma separated list of cohort names" + UP_TO_100; + public static final String COHORT_IDS_DESCRIPTION = "Comma separated list of cohort IDs" + UP_TO_100 + REGEX_SUPPORT; + public static final String COHORT_NAMES_DESCRIPTION = "Comma separated list of cohort names" + UP_TO_100 + REGEX_SUPPORT; public static final String COHORT_UUIDS_DESCRIPTION = "Comma separated list of cohort IDs" + UP_TO_100; - public static final String CLINICAL_ID_DESCRIPTION = "Comma separated list of Clinical Analysis IDs" + UP_TO_100; + public static final String CLINICAL_ID_DESCRIPTION = "Comma separated list of Clinical Analysis IDs" + UP_TO_100 + REGEX_SUPPORT; public static final String CLINICAL_UUID_DESCRIPTION = "Comma separated list of Clinical Analysis UUIDs" + UP_TO_100; public static final String CLINICAL_ANALYSES_DESCRIPTION = "Comma separated list of clinical analysis IDs or names" + UP_TO_100; - public static final String INTERPRETATION_ID_DESCRIPTION = "Comma separated list of Interpretation IDs" + UP_TO_100; + public static final String INTERPRETATION_ID_DESCRIPTION = "Comma separated list of Interpretation IDs" + UP_TO_100 + REGEX_SUPPORT; public static final String INTERPRETATION_UUID_DESCRIPTION = "Comma separated list of Interpretation UUIDs" + UP_TO_100; public static final String INTERPRETATION_DESCRIPTION = "Comma separated list of clinical interpretation IDs " + UP_TO_100; - public static final String PANEL_ID_DESCRIPTION = "Comma separated list of panel IDs " + UP_TO_100; + public static final String PANEL_ID_DESCRIPTION = "Comma separated list of panel IDs " + UP_TO_100 + REGEX_SUPPORT; public static final String PANEL_UUID_DESCRIPTION = "Comma separated list of panel UUIDs " + UP_TO_100; - public static final String PANEL_NAME_DESCRIPTION = "Comma separated list of panel names " + UP_TO_100; + public static final String PANEL_NAME_DESCRIPTION = "Comma separated list of panel names " + UP_TO_100 + REGEX_SUPPORT; public static final String JOBS_DESCRIPTION = "Comma separated list of job IDs or UUIDs" + UP_TO_100; - public static final String JOB_IDS_DESCRIPTION = "Comma separated list of job IDs" + UP_TO_100; + public static final String JOB_IDS_DESCRIPTION = "Comma separated list of job IDs" + UP_TO_100 + REGEX_SUPPORT; public static final String JOB_UUIDS_DESCRIPTION = "Comma separated list of job UUIDs" + UP_TO_100; // --------------------------------------------- public static final String PROJECTS_DESCRIPTION = "Comma separated list of projects [user@]project" + UP_TO_100; From b677b547a00bb4c30a49e33a3f30f2af45780379 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?= Date: Mon, 28 Aug 2023 11:22:00 +0200 Subject: [PATCH 087/109] core: update according to CellBase changes, #TASK-4898, #TASK-4641 --- .../alignment/AlignmentStorageManager.java | 4 +-- .../manager/VariantStorageManager.java | 4 +-- .../opencga/core/api/ParamConstants.java | 2 +- .../core/cellbase/CellBaseValidator.java | 17 +++++------ .../config/storage/CellBaseConfiguration.java | 29 +++++++++++++----- .../core/variant/VariantStorageEngine.java | 2 +- .../AbstractCellBaseVariantAnnotator.java | 2 +- .../CellBaseRestVariantAnnotator.java | 4 +-- ...java => VariantAnnotatorByApiKeyTest.java} | 30 +++++++++---------- .../annotators/VariantAnnotatorTest.java | 11 ++----- 10 files changed, 57 insertions(+), 48 deletions(-) rename opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/{VariantAnnotatorByTokenTest.java => VariantAnnotatorByApiKeyTest.java} (87%) diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentStorageManager.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentStorageManager.java index 38953f5ff7f..fd8a0cebad5 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentStorageManager.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentStorageManager.java @@ -230,7 +230,7 @@ public OpenCGAResult coverageStats(String studyIdStr, String String species = projectQueryResult.first().getOrganism().getScientificName(); String assembly = projectQueryResult.first().getOrganism().getAssembly(); String dataRelease = projectQueryResult.first().getCellbase().getDataRelease(); - String cellbaseToken = projectQueryResult.first().getCellbase().getToken(); + String cellbaseToken = projectQueryResult.first().getCellbase().getApiKey(); for (String geneName : geneNames) { @@ -451,7 +451,7 @@ public List mergeRegions(List regions, List genes, boole String species = projectQueryResult.first().getOrganism().getScientificName(); String assembly = projectQueryResult.first().getOrganism().getAssembly(); String dataRelease = projectQueryResult.first().getCellbase().getDataRelease(); - String cellbaseToken = projectQueryResult.first().getCellbase().getToken(); + String cellbaseToken = projectQueryResult.first().getCellbase().getApiKey(); CellBaseClient cellBaseClient = new CellBaseClient(species, assembly, dataRelease, cellbaseToken, projectQueryResult.first().getCellbase().toClientConfiguration()); GeneClient geneClient = cellBaseClient.getGeneClient(); diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java index 806fbb6d818..b017ec0698c 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java @@ -1017,8 +1017,8 @@ private void setCellbaseConfiguration(VariantStorageEngine engine, String projec .get(project, new QueryOptions(INCLUDE, ProjectDBAdaptor.QueryParams.CELLBASE.key()), token) .first().getCellbase(); if (cellbase != null) { - if (StringUtils.isEmpty(cellbase.getToken()) || storageConfiguration.getCellbase() != null) { - cellbase.setToken(storageConfiguration.getCellbase().getToken()); + if (StringUtils.isEmpty(cellbase.getApiKey()) || storageConfiguration.getCellbase() != null) { + cellbase.setApiKey(storageConfiguration.getCellbase().getApiKey()); } engine.getConfiguration().setCellbase(cellbase); engine.reloadCellbaseConfiguration(); diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java b/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java index b65214a9ba4..b1e57dbc24a 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java @@ -76,7 +76,7 @@ public class ParamConstants { public static final String CELLBASE_URL = "https://ws.zettagenomics.com/cellbase"; public static final String CELLBASE_VERSION = "v5.1"; public static final String CELLBASE_DATA_RELEASE = "2"; - public static final String CELLBASE_TOKEN = ""; + public static final String CELLBASE_APIKEY = ""; public static final String POP_FREQ_1000G_CB_V4 = "1kG_phase3"; public static final String POP_FREQ_1000G_CB_V5 = "1000G"; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java b/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java index 21f5c79fecd..83f1bd9e311 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java @@ -2,12 +2,11 @@ import org.apache.commons.lang3.StringUtils; import org.opencb.cellbase.client.rest.CellBaseClient; +import org.opencb.cellbase.core.api.key.ApiKeyManager; import org.opencb.cellbase.core.config.SpeciesConfiguration; import org.opencb.cellbase.core.config.SpeciesProperties; import org.opencb.cellbase.core.models.DataRelease; import org.opencb.cellbase.core.result.CellBaseDataResponse; -import org.opencb.cellbase.core.token.DataAccessTokenManager; -import org.opencb.cellbase.core.token.DataAccessTokenSources; import org.opencb.opencga.core.common.VersionUtils; import org.opencb.opencga.core.config.storage.CellBaseConfiguration; import org.slf4j.Logger; @@ -69,13 +68,13 @@ public String getDataRelease() { return cellBaseClient.getDataRelease(); } - public String getToken() { - return cellBaseClient.getToken(); + public String getApiKey() { + return cellBaseClient.getApiKey(); } - public DataAccessTokenSources getTokenSources() { - DataAccessTokenManager tokenManager = new DataAccessTokenManager(); - return tokenManager.decode(cellBaseClient.getToken()); + public List getApiKeyDataSources() { + ApiKeyManager apiKeyManager = new ApiKeyManager(); + return new ArrayList<>(apiKeyManager.getValidSources(cellBaseClient.getApiKey())); } public String getURL() { @@ -91,7 +90,7 @@ public CellBaseClient getCellBaseClient() { } public CellBaseConfiguration getCellBaseConfiguration() { - return new CellBaseConfiguration(getURL(), getVersion(), getDataRelease(), getToken()); + return new CellBaseConfiguration(getURL(), getVersion(), getDataRelease(), getApiKey()); } public String getDefaultDataRelease() throws IOException { @@ -281,7 +280,7 @@ public String toString() { + "species '" + getSpecies() + "', " + "assembly '" + getAssembly() + "', " + "dataRelease '" + getDataRelease() + "', " - + "token '" + getToken() + "'"; + + "token '" + getApiKey() + "'"; } } diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/CellBaseConfiguration.java b/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/CellBaseConfiguration.java index 9a392c88168..1818beb363c 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/CellBaseConfiguration.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/CellBaseConfiguration.java @@ -42,9 +42,13 @@ public class CellBaseConfiguration { @DataField(id = "dataRelease", description = "CellBase data release version to be used. If empty, will use the active one") private String dataRelease; - @DataField(id = "token", description = "CellBase token to access to the licensed/restricted data sources such as COSMIC, HGMD,...") + @Deprecated + @DataField(id = "token", deprecated = true, description = "CellBase token to access to the licensed/restricted data sources such as COSMIC, HGMD,...") private String token; + @DataField(id = "apiKey", description = "API key to access to the licensed/restricted data sources (COSMIC, HGMD,...) and to manage quota.") + private String apiKey; + public CellBaseConfiguration() { this(ParamConstants.CELLBASE_URL, ParamConstants.CELLBASE_VERSION); } @@ -54,11 +58,12 @@ public CellBaseConfiguration(String url, String version) { this.version = version; } - public CellBaseConfiguration(String url, String version, String dataRelease, String token) { + public CellBaseConfiguration(String url, String version, String dataRelease, String apiKey) { this.url = url; this.version = version; this.dataRelease = dataRelease; - this.token = token; + this.token = apiKey; + this.apiKey = apiKey; } @Override @@ -68,6 +73,7 @@ public String toString() { sb.append(", version='").append(version).append('\''); sb.append(", dataRelease='").append(dataRelease).append('\''); sb.append(", token='").append(token).append('\''); + sb.append(", apiKey='").append(apiKey).append('\''); sb.append('}'); return sb.toString(); } @@ -99,12 +105,21 @@ public CellBaseConfiguration setDataRelease(String dataRelease) { return this; } - public String getToken() { - return token; +// public String getToken() { +// return apiKey; +// } +// +// public CellBaseConfiguration setToken(String token) { +// this.apiKey = token; +// return this; +// } + + public String getApiKey() { + return apiKey; } - public CellBaseConfiguration setToken(String token) { - this.token = token; + public CellBaseConfiguration setApiKey(String apiKey) { + this.apiKey = apiKey; return this; } diff --git a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/VariantStorageEngine.java b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/VariantStorageEngine.java index c3c27c26c35..a4f560e49f2 100644 --- a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/VariantStorageEngine.java +++ b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/VariantStorageEngine.java @@ -1117,7 +1117,7 @@ public CellBaseUtils getCellBaseUtils() throws StorageEngineException { } species = toCellBaseSpeciesName(species); cellBaseUtils = new CellBaseUtils(new CellBaseClient(species, assembly, configuration.getCellbase().getDataRelease(), - configuration.getCellbase().getToken(), clientConfiguration)); + configuration.getCellbase().getApiKey(), clientConfiguration)); } return cellBaseUtils; } diff --git a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/AbstractCellBaseVariantAnnotator.java b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/AbstractCellBaseVariantAnnotator.java index 320c909c33a..fc743b13a76 100644 --- a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/AbstractCellBaseVariantAnnotator.java +++ b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/AbstractCellBaseVariantAnnotator.java @@ -72,7 +72,7 @@ public AbstractCellBaseVariantAnnotator(StorageConfiguration storageConfiguratio assembly = projectMetadata.getAssembly(); cellbaseVersion = storageConfiguration.getCellbase().getVersion(); cellbaseDataRelease = storageConfiguration.getCellbase().getDataRelease(); - cellbaseToken = storageConfiguration.getCellbase().getToken(); + cellbaseToken = storageConfiguration.getCellbase().getApiKey(); queryOptions = new QueryOptions(); if (StringUtils.isNotEmpty(params.getString(VariantStorageOptions.ANNOTATOR_CELLBASE_INCLUDE.key()))) { diff --git a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/CellBaseRestVariantAnnotator.java b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/CellBaseRestVariantAnnotator.java index 889cba2f42a..85ee3b0810c 100644 --- a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/CellBaseRestVariantAnnotator.java +++ b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/CellBaseRestVariantAnnotator.java @@ -113,8 +113,8 @@ public ProjectMetadata.VariantAnnotationMetadata getVariantAnnotationMetadata() + getDebugInfo("/meta/" + species + "/dataReleases") + ". "); } List privateSources; - if (StringUtils.isNotEmpty(cellBaseUtils.getToken())) { - privateSources = new ArrayList<>(cellBaseUtils.getTokenSources().getSources().keySet()); + if (StringUtils.isNotEmpty(cellBaseUtils.getApiKey())) { + privateSources = cellBaseUtils.getApiKeyDataSources(); } else { privateSources = new ArrayList<>(); } diff --git a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/VariantAnnotatorByTokenTest.java b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/VariantAnnotatorByApiKeyTest.java similarity index 87% rename from opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/VariantAnnotatorByTokenTest.java rename to opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/VariantAnnotatorByApiKeyTest.java index 0faf42d6cb7..806a75df2fb 100644 --- a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/VariantAnnotatorByTokenTest.java +++ b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/VariantAnnotatorByApiKeyTest.java @@ -21,7 +21,7 @@ import static org.junit.Assert.assertEquals; import static org.opencb.opencga.storage.core.variant.VariantStorageOptions.ANNOTATOR_CELLBASE_INCLUDE; -public class VariantAnnotatorByTokenTest { +public class VariantAnnotatorByApiKeyTest { private StorageConfiguration storageConfiguration; @@ -36,7 +36,7 @@ public void setUp() throws Exception { storageConfiguration.getCellbase().setUrl(url); storageConfiguration.getCellbase().setDataRelease("1"); storageConfiguration.getCellbase().setVersion("v5.3"); - storageConfiguration.getCellbase().setToken(null); + storageConfiguration.getCellbase().setApiKey(null); CellBaseUtils cellBaseUtils = new CellBaseUtils(new CellBaseClient(storageConfiguration.getCellbase().toClientConfiguration())); try { @@ -47,7 +47,7 @@ public void setUp() throws Exception { } @Test - public void testNoToken() throws Exception { + public void testNoApiKey() throws Exception { projectMetadata = new ProjectMetadata("hsapiens", "grch37", "1", 1, null, null, null); ObjectMap options = new ObjectMap(VariantStorageOptions.ANNOTATOR.key(), "cellbase"); CellBaseRestVariantAnnotator annotator = new CellBaseRestVariantAnnotator(storageConfiguration, projectMetadata, options); @@ -61,11 +61,11 @@ public void testNoToken() throws Exception { } @Test - public void testCOSMICToken() throws Exception { - String cosmicToken = System.getenv("CELLBASE_COSMIC_TOKEN"); - Assume.assumeTrue(StringUtils.isNotEmpty(cosmicToken)); + public void testCOSMICApiKey() throws Exception { + String apiKey = System.getenv("CELLBASE_COSMIC_APIKEY"); + Assume.assumeTrue(StringUtils.isNotEmpty(apiKey)); - storageConfiguration.getCellbase().setToken(cosmicToken); + storageConfiguration.getCellbase().setApiKey(apiKey); projectMetadata = new ProjectMetadata("hsapiens", "grch37", "1", 1, null, null, null); ObjectMap options = new ObjectMap(VariantStorageOptions.ANNOTATOR.key(), "cellbase"); CellBaseRestVariantAnnotator annotator = new CellBaseRestVariantAnnotator(storageConfiguration, projectMetadata, options); @@ -80,11 +80,11 @@ public void testCOSMICToken() throws Exception { } @Test - public void testHGMDToken() throws Exception { - String hgmdToken = System.getenv("CELLBASE_HGMD_TOKEN"); - Assume.assumeTrue(StringUtils.isNotEmpty(hgmdToken)); + public void testHGMDApiKey() throws Exception { + String apiKey = System.getenv("CELLBASE_HGMD_APIKEY"); + Assume.assumeTrue(StringUtils.isNotEmpty(apiKey)); - storageConfiguration.getCellbase().setToken(hgmdToken); + storageConfiguration.getCellbase().setApiKey(apiKey); projectMetadata = new ProjectMetadata("hsapiens", "grch37", "1", 1, null, null, null); ObjectMap options = new ObjectMap(VariantStorageOptions.ANNOTATOR.key(), "cellbase"); CellBaseRestVariantAnnotator annotator = new CellBaseRestVariantAnnotator(storageConfiguration, projectMetadata, options); @@ -99,11 +99,11 @@ public void testHGMDToken() throws Exception { } @Test - public void testCOSMICandHGMDToken() throws Exception { - String token = System.getenv("CELLBASE_TOKEN"); - Assume.assumeTrue(StringUtils.isNotEmpty(token)); + public void testCOSMICandHGMDApiKey() throws Exception { + String apiKey = System.getenv("CELLBASE_COSMIC_HGMD_APIKEY"); + Assume.assumeTrue(StringUtils.isNotEmpty(apiKey)); - storageConfiguration.getCellbase().setToken(token); + storageConfiguration.getCellbase().setApiKey(apiKey); projectMetadata = new ProjectMetadata("hsapiens", "grch37", "1", 1, null, null, null); ObjectMap options = new ObjectMap(VariantStorageOptions.ANNOTATOR.key(), "cellbase"); diff --git a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/VariantAnnotatorTest.java b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/VariantAnnotatorTest.java index cf2b4201b5f..260e1840dba 100644 --- a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/VariantAnnotatorTest.java +++ b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/VariantAnnotatorTest.java @@ -9,20 +9,15 @@ import org.opencb.biodata.models.variant.Variant; import org.opencb.biodata.models.variant.avro.EvidenceEntry; import org.opencb.biodata.models.variant.avro.VariantAnnotation; -import org.opencb.cellbase.client.config.ClientConfiguration; -import org.opencb.cellbase.client.config.RestConfig; -import org.opencb.cellbase.client.rest.CellBaseClient; import org.opencb.cellbase.core.result.CellBaseDataResult; import org.opencb.commons.datastore.core.ObjectMap; import org.opencb.opencga.core.testclassification.duration.ShortTests; import org.opencb.opencga.storage.core.StorageEngine; import org.opencb.opencga.core.config.storage.StorageConfiguration; import org.opencb.opencga.storage.core.metadata.models.ProjectMetadata; -import org.opencb.opencga.storage.core.utils.CellBaseUtils; import org.opencb.opencga.storage.core.variant.VariantStorageOptions; import org.opencb.opencga.storage.core.variant.annotation.VariantAnnotatorException; -import java.io.IOException; import java.util.*; import static org.hamcrest.CoreMatchers.instanceOf; @@ -139,7 +134,7 @@ public void useCellBaseTokens() throws VariantAnnotatorException { assertFalse(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("hgmd"))); // Using COSMIC token - storageConfiguration.getCellbase().setToken("eyJhbGciOiJIUzI1NiJ9.eyJzb3VyY2VzIjp7ImNvc21pYyI6OTIyMzM3MjAzNjg1NDc3NTgwN30sInZlcnNpb24iOiIxLjAiLCJzdWIiOiJaRVRUQSIsImlhdCI6MTY3NTg3MjQ2Nn0.ByfPJn8Lkh5Sow4suRZcOqVxvWZRmTBBNLDzHEIZQ5U"); + storageConfiguration.getCellbase().setApiKey("eyJhbGciOiJIUzI1NiJ9.eyJzb3VyY2VzIjp7ImNvc21pYyI6OTIyMzM3MjAzNjg1NDc3NTgwN30sInZlcnNpb24iOiIxLjAiLCJzdWIiOiJaRVRUQSIsImlhdCI6MTY3NTg3MjQ2Nn0.ByfPJn8Lkh5Sow4suRZcOqVxvWZRmTBBNLDzHEIZQ5U"); variantAnnotator = VariantAnnotatorFactory.buildVariantAnnotator(storageConfiguration, projectMetadata, options); results = variantAnnotator.annotate(Collections.singletonList(new Variant("10:113588287:G:A"))); assertEquals(1, results.size()); @@ -148,7 +143,7 @@ public void useCellBaseTokens() throws VariantAnnotatorException { assertFalse(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("hgmd"))); // Using HGMD token - storageConfiguration.getCellbase().setToken("eyJhbGciOiJIUzI1NiJ9.eyJzb3VyY2VzIjp7ImhnbWQiOjkyMjMzNzIwMzY4NTQ3NzU4MDd9LCJ2ZXJzaW9uIjoiMS4wIiwic3ViIjoiWkVUVEEiLCJpYXQiOjE2NzU4NzI1MDd9.f3JgVRt7_VrifNWTaRMW3aQfrKbtDbIxlzoenJRYJo0"); + storageConfiguration.getCellbase().setApiKey("eyJhbGciOiJIUzI1NiJ9.eyJzb3VyY2VzIjp7ImhnbWQiOjkyMjMzNzIwMzY4NTQ3NzU4MDd9LCJ2ZXJzaW9uIjoiMS4wIiwic3ViIjoiWkVUVEEiLCJpYXQiOjE2NzU4NzI1MDd9.f3JgVRt7_VrifNWTaRMW3aQfrKbtDbIxlzoenJRYJo0"); variantAnnotator = VariantAnnotatorFactory.buildVariantAnnotator(storageConfiguration, projectMetadata, options); results = variantAnnotator.annotate(Collections.singletonList(new Variant("10:113588287:G:A"))); assertEquals(1, results.size()); @@ -157,7 +152,7 @@ public void useCellBaseTokens() throws VariantAnnotatorException { assertTrue(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("hgmd"))); // Using COSMIC = HGMD token - storageConfiguration.getCellbase().setToken("eyJhbGciOiJIUzI1NiJ9.eyJzb3VyY2VzIjp7ImNvc21pYyI6OTIyMzM3MjAzNjg1NDc3NTgwNywiaGdtZCI6OTIyMzM3MjAzNjg1NDc3NTgwN30sInZlcnNpb24iOiIxLjAiLCJzdWIiOiJaRVRUQSIsImlhdCI6MTY3NTg3MjUyN30.NCCFc4SAhjUsN5UU0wXGY6nCZx8jLglvaO1cNZYI0u4"); + storageConfiguration.getCellbase().setApiKey("eyJhbGciOiJIUzI1NiJ9.eyJzb3VyY2VzIjp7ImNvc21pYyI6OTIyMzM3MjAzNjg1NDc3NTgwNywiaGdtZCI6OTIyMzM3MjAzNjg1NDc3NTgwN30sInZlcnNpb24iOiIxLjAiLCJzdWIiOiJaRVRUQSIsImlhdCI6MTY3NTg3MjUyN30.NCCFc4SAhjUsN5UU0wXGY6nCZx8jLglvaO1cNZYI0u4"); variantAnnotator = VariantAnnotatorFactory.buildVariantAnnotator(storageConfiguration, projectMetadata, options); results = variantAnnotator.annotate(Collections.singletonList(new Variant("10:113588287:G:A"))); assertEquals(1, results.size()); From cb2e78bf8c06caac1facf09114920d4f923bb244 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?= Date: Tue, 29 Aug 2023 12:02:59 +0200 Subject: [PATCH 088/109] tests: remove VersionUtils and use it from java-commons-lib, and fix some tests using CellBase API keys, #TASK-4898, #TASK-4641 --- .../core/cellbase/CellBaseValidator.java | 2 +- .../opencga/core/common/VersionUtils.java | 123 ------------------ .../opencga/core/common/VersionUtilsTest.java | 35 ----- .../storage/core/utils/CellBaseUtilsTest.java | 20 +-- .../VariantAnnotatorByApiKeyTest.java | 18 +-- .../annotators/VariantAnnotatorTest.java | 68 +++++----- 6 files changed, 53 insertions(+), 213 deletions(-) delete mode 100644 opencga-core/src/main/java/org/opencb/opencga/core/common/VersionUtils.java delete mode 100644 opencga-core/src/test/java/org/opencb/opencga/core/common/VersionUtilsTest.java diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java b/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java index 83f1bd9e311..dd8988e761b 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java @@ -7,7 +7,7 @@ import org.opencb.cellbase.core.config.SpeciesProperties; import org.opencb.cellbase.core.models.DataRelease; import org.opencb.cellbase.core.result.CellBaseDataResponse; -import org.opencb.opencga.core.common.VersionUtils; +import org.opencb.commons.utils.VersionUtils; import org.opencb.opencga.core.config.storage.CellBaseConfiguration; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/common/VersionUtils.java b/opencga-core/src/main/java/org/opencb/opencga/core/common/VersionUtils.java deleted file mode 100644 index 4e32c6ada32..00000000000 --- a/opencga-core/src/main/java/org/opencb/opencga/core/common/VersionUtils.java +++ /dev/null @@ -1,123 +0,0 @@ -package org.opencb.opencga.core.common; - -import org.apache.commons.lang3.StringUtils; - -import java.util.Comparator; -import java.util.List; -import java.util.stream.Collectors; - -public class VersionUtils { - - public static List order(List versions) { - return versions.stream().map(Version::new).sorted().map(Version::toString).collect(Collectors.toList()); - } - - public static boolean isMinVersion(String minVersion, String version) { - return isMinVersion(minVersion, version, false); - } - - public static boolean isMinVersion(String minVersion, String version, boolean ignorePreReleaseVersioning) { - return new Version(minVersion).compareTo(new Version(version), ignorePreReleaseVersioning) <= 0; - } - - public static class Version implements Comparable { - - private final int major; - private final int minor; - private final int patch; - private final int repatch; - private final String other; - - public static final Comparator COMPARATOR = Comparator - .comparingInt(Version::getMajor) - .thenComparingInt(Version::getMinor) - .thenComparingInt(Version::getPatch) - .thenComparingInt(Version::getRepatch) - .thenComparing((o1, o2) -> { - if (o1.other.equals(o2.other)) { - return 0; - } - if (o1.other.isEmpty()) { - return +1; - } - if (o2.other.isEmpty()) { - return -1; - } - if (o1.other.equals("-SNAPSHOT")) { - return -1; - } - if (o2.other.equals("-SNAPSHOT")) { - return +1; - } - return o1.other.compareTo(o2.other); - }); - - public static final Comparator COMPARATOR_NO_PR = Comparator - .comparingInt(Version::getMajor) - .thenComparingInt(Version::getMinor) - .thenComparingInt(Version::getPatch) - .thenComparingInt(Version::getRepatch); - - public Version(String version) { - String[] split = StringUtils.split(version, ".", 4); - major = Integer.parseInt(split[0]); - minor = Integer.parseInt(split[1]); - if (split.length == 4) { - patch = Integer.parseInt(split[2]); - String last = split[3]; - String[] split2 = StringUtils.split(last, "-+", 3); - repatch = Integer.parseInt(split2[0]); - other = last.substring(split2[0].length()); - } else { - String last = split[2]; - String[] split2 = StringUtils.split(last, "-+", 2); - patch = Integer.parseInt(split2[0]); - repatch = 0; - other = last.substring(split2[0].length()); - } - } - - @Override - public String toString() { - if (repatch > 0) { - return major + "." + minor + "." + patch + "." + repatch + other; - } else { - return major + "." + minor + "." + patch + other; - } - } - - @Override - public int compareTo(Version o) { - return COMPARATOR.compare(this, o); - } - - public int compareTo(Version o, boolean ignorePreReleaseVersioning) { - if (ignorePreReleaseVersioning) { - return COMPARATOR_NO_PR.compare(this, o); - } else { - return COMPARATOR.compare(this, o); - } - } - - public int getMajor() { - return major; - } - - public int getMinor() { - return minor; - } - - public int getPatch() { - return patch; - } - - public int getRepatch() { - return repatch; - } - - public String getOther() { - return other; - } - } - -} diff --git a/opencga-core/src/test/java/org/opencb/opencga/core/common/VersionUtilsTest.java b/opencga-core/src/test/java/org/opencb/opencga/core/common/VersionUtilsTest.java deleted file mode 100644 index a6b0dce858f..00000000000 --- a/opencga-core/src/test/java/org/opencb/opencga/core/common/VersionUtilsTest.java +++ /dev/null @@ -1,35 +0,0 @@ -package org.opencb.opencga.core.common; - -import org.junit.Assert; -import org.junit.Test; -import org.junit.experimental.categories.Category; -import org.opencb.opencga.core.testclassification.duration.ShortTests; - -@Category(ShortTests.class) -public class VersionUtilsTest { - public static String getComparation(String minVersion, String version) { - int c = new VersionUtils.Version(minVersion).compareTo(new VersionUtils.Version(version)); - String comp; - if (c == 0) { - comp = "="; - } else if (c < 0) { - comp = "<"; - } else { - comp = ">"; - } - System.out.println(minVersion + "\t" + comp + "\t" + version); - return comp; - } - - @Test - public void testOrder() { - Assert.assertEquals("<", getComparation("5.2.7", "5.2.8")); - Assert.assertEquals("=", getComparation("5.2.7", "5.2.7")); - Assert.assertEquals(">", getComparation("5.2.7.1", "5.2.7.1-alpha")); - Assert.assertEquals(">", getComparation("5.2.7", "5.2.7-SNAPSHOT")); - Assert.assertEquals("<", getComparation("5.2.7-alpha", "5.2.7")); - Assert.assertEquals("<", getComparation("5.2.7-alpha", "5.2.7-beta")); - Assert.assertEquals(">", getComparation("5.2.7", "5.2.6")); - Assert.assertEquals("=", getComparation("5.2.7", "5.2.7.0")); - } -} \ No newline at end of file diff --git a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/utils/CellBaseUtilsTest.java b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/utils/CellBaseUtilsTest.java index 1f679ace47e..93cb92e8899 100644 --- a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/utils/CellBaseUtilsTest.java +++ b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/utils/CellBaseUtilsTest.java @@ -21,7 +21,7 @@ import org.opencb.commons.datastore.core.ObjectMap; import org.opencb.commons.datastore.core.Query; import org.opencb.commons.datastore.core.QueryOptions; -import org.opencb.opencga.core.common.VersionUtils; +import org.opencb.commons.utils.VersionUtils; import org.opencb.opencga.core.testclassification.duration.MediumTests; import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryException; import org.opencb.opencga.storage.core.variant.adaptors.VariantQueryParam; @@ -255,10 +255,10 @@ public void testGetTranscriptFlags() throws IOException { } @Test - public void testAnnotationWithHGMDToken() throws IOException { - Assume.assumeTrue(cellBaseUtils.isMinVersion("5.3.0")); - Assume.assumeThat(assembly, CoreMatchers.equalTo("grch37")); - String hgmdToken = System.getenv("CELLBASE_HGMD_TOKEN"); + public void testAnnotationWithHGMDApiKey() throws IOException { + Assume.assumeTrue(cellBaseUtils.isMinVersion("5.4.0")); + Assume.assumeThat(assembly, CoreMatchers.equalTo("grch38")); + String hgmdToken = System.getenv("CELLBASE_HGMD_APIKEY"); Assume.assumeTrue(StringUtils.isNotEmpty(hgmdToken)); cellBaseClient = new CellBaseClient("hsapiens", assembly, dataRelease, hgmdToken, @@ -271,14 +271,14 @@ public void testAnnotationWithHGMDToken() throws IOException { .getAnnotationByVariantIds(Collections.singletonList("10:113588287:G:A"), queryOptions); VariantAnnotation variantAnnotation = v.firstResult(); assertEquals(2, variantAnnotation.getTraitAssociation().size()); - assertEquals("clinvar", variantAnnotation.getTraitAssociation().get(0).getSource().getName()); - assertEquals("hgmd", variantAnnotation.getTraitAssociation().get(1).getSource().getName()); + assertTrue(variantAnnotation.getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("clinvar"))); + assertTrue(variantAnnotation.getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("hgmd"))); } @Test - public void testAnnotationWithoutHGMDToken() throws IOException { - Assume.assumeTrue(cellBaseUtils.isMinVersion("5.3.0")); - Assume.assumeThat(assembly, CoreMatchers.equalTo("grch37")); + public void testAnnotationWithoutHGMDAPiKey() throws IOException { + Assume.assumeTrue(cellBaseUtils.isMinVersion("5.4.0")); + Assume.assumeThat(assembly, CoreMatchers.equalTo("grch38")); cellBaseClient = new CellBaseClient("hsapiens", assembly, dataRelease, "", new ClientConfiguration().setVersion(version) diff --git a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/VariantAnnotatorByApiKeyTest.java b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/VariantAnnotatorByApiKeyTest.java index 806a75df2fb..02ae9aded18 100644 --- a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/VariantAnnotatorByApiKeyTest.java +++ b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/VariantAnnotatorByApiKeyTest.java @@ -34,21 +34,18 @@ public void setUp() throws Exception { storageConfiguration = StorageConfiguration.load(StorageEngine.class.getClassLoader().getResourceAsStream("storage-configuration.yml"), "yml"); String url = "https://uk.ws.zettagenomics.com/cellbase/"; storageConfiguration.getCellbase().setUrl(url); - storageConfiguration.getCellbase().setDataRelease("1"); - storageConfiguration.getCellbase().setVersion("v5.3"); + storageConfiguration.getCellbase().setDataRelease("3"); + storageConfiguration.getCellbase().setVersion("v5.4"); storageConfiguration.getCellbase().setApiKey(null); CellBaseUtils cellBaseUtils = new CellBaseUtils(new CellBaseClient(storageConfiguration.getCellbase().toClientConfiguration())); - try { - Assume.assumeTrue(cellBaseUtils.isMinVersion("5.3.0")); - } catch (RuntimeException e) { - Assume.assumeNoException("Cellbase '" + url + "' not available", e); - } + Assume.assumeTrue(cellBaseUtils.isMinVersion("v5.4")); + + projectMetadata = new ProjectMetadata("hsapiens", "grch38", "3", 1, null, null, null); } @Test public void testNoApiKey() throws Exception { - projectMetadata = new ProjectMetadata("hsapiens", "grch37", "1", 1, null, null, null); ObjectMap options = new ObjectMap(VariantStorageOptions.ANNOTATOR.key(), "cellbase"); CellBaseRestVariantAnnotator annotator = new CellBaseRestVariantAnnotator(storageConfiguration, projectMetadata, options); @@ -66,7 +63,7 @@ public void testCOSMICApiKey() throws Exception { Assume.assumeTrue(StringUtils.isNotEmpty(apiKey)); storageConfiguration.getCellbase().setApiKey(apiKey); - projectMetadata = new ProjectMetadata("hsapiens", "grch37", "1", 1, null, null, null); + ObjectMap options = new ObjectMap(VariantStorageOptions.ANNOTATOR.key(), "cellbase"); CellBaseRestVariantAnnotator annotator = new CellBaseRestVariantAnnotator(storageConfiguration, projectMetadata, options); assertEquals(Collections.singletonList("cosmic"), annotator.getVariantAnnotationMetadata().getPrivateSources()); @@ -85,7 +82,7 @@ public void testHGMDApiKey() throws Exception { Assume.assumeTrue(StringUtils.isNotEmpty(apiKey)); storageConfiguration.getCellbase().setApiKey(apiKey); - projectMetadata = new ProjectMetadata("hsapiens", "grch37", "1", 1, null, null, null); + ObjectMap options = new ObjectMap(VariantStorageOptions.ANNOTATOR.key(), "cellbase"); CellBaseRestVariantAnnotator annotator = new CellBaseRestVariantAnnotator(storageConfiguration, projectMetadata, options); assertEquals(Collections.singletonList("hgmd"), annotator.getVariantAnnotationMetadata().getPrivateSources()); @@ -105,7 +102,6 @@ public void testCOSMICandHGMDApiKey() throws Exception { storageConfiguration.getCellbase().setApiKey(apiKey); - projectMetadata = new ProjectMetadata("hsapiens", "grch37", "1", 1, null, null, null); ObjectMap options = new ObjectMap(VariantStorageOptions.ANNOTATOR.key(), "cellbase"); options.put(ANNOTATOR_CELLBASE_INCLUDE.key(), "clinical"); CellBaseRestVariantAnnotator annotator = new CellBaseRestVariantAnnotator(storageConfiguration, projectMetadata, options); diff --git a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/VariantAnnotatorTest.java b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/VariantAnnotatorTest.java index 260e1840dba..02b84fc38a9 100644 --- a/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/VariantAnnotatorTest.java +++ b/opencga-storage/opencga-storage-core/src/test/java/org/opencb/opencga/storage/core/variant/annotation/annotators/VariantAnnotatorTest.java @@ -1,6 +1,7 @@ package org.opencb.opencga.storage.core.variant.annotation.annotators; import org.apache.commons.collections4.CollectionUtils; +import org.apache.commons.lang.StringUtils; import org.junit.Before; import org.junit.Rule; import org.junit.Test; @@ -111,9 +112,9 @@ public void testErrorVariant() throws VariantAnnotatorException { } @Test - public void useCellBaseTokens() throws VariantAnnotatorException { + public void useCellBaseApiKeys() throws VariantAnnotatorException { storageConfiguration.getCellbase().setUrl("https://uk.ws.zettagenomics.com/cellbase/"); - storageConfiguration.getCellbase().setVersion("task-3808"); + storageConfiguration.getCellbase().setVersion("v5.4"); storageConfiguration.getCellbase().setDataRelease("3"); VariantAnnotator variantAnnotator = null; @@ -126,6 +127,8 @@ public void useCellBaseTokens() throws VariantAnnotatorException { } assumeTrue(variantAnnotator != null); + String apiKey; + // No token List results = variantAnnotator.annotate(Collections.singletonList(new Variant("10:113588287:G:A"))); assertEquals(1, results.size()); @@ -134,41 +137,40 @@ public void useCellBaseTokens() throws VariantAnnotatorException { assertFalse(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("hgmd"))); // Using COSMIC token - storageConfiguration.getCellbase().setApiKey("eyJhbGciOiJIUzI1NiJ9.eyJzb3VyY2VzIjp7ImNvc21pYyI6OTIyMzM3MjAzNjg1NDc3NTgwN30sInZlcnNpb24iOiIxLjAiLCJzdWIiOiJaRVRUQSIsImlhdCI6MTY3NTg3MjQ2Nn0.ByfPJn8Lkh5Sow4suRZcOqVxvWZRmTBBNLDzHEIZQ5U"); - variantAnnotator = VariantAnnotatorFactory.buildVariantAnnotator(storageConfiguration, projectMetadata, options); - results = variantAnnotator.annotate(Collections.singletonList(new Variant("10:113588287:G:A"))); - assertEquals(1, results.size()); - assertTrue(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("clinvar"))); - assertTrue(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("cosmic"))); - assertFalse(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("hgmd"))); + apiKey = System.getenv("CELLBASE_COSMIC_APIKEY"); + if (StringUtils.isNotEmpty(apiKey)) { + storageConfiguration.getCellbase().setApiKey(apiKey); + variantAnnotator = VariantAnnotatorFactory.buildVariantAnnotator(storageConfiguration, projectMetadata, options); + results = variantAnnotator.annotate(Collections.singletonList(new Variant("10:113588287:G:A"))); + assertEquals(1, results.size()); + assertTrue(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("clinvar"))); + assertTrue(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("cosmic"))); + assertFalse(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("hgmd"))); + } // Using HGMD token - storageConfiguration.getCellbase().setApiKey("eyJhbGciOiJIUzI1NiJ9.eyJzb3VyY2VzIjp7ImhnbWQiOjkyMjMzNzIwMzY4NTQ3NzU4MDd9LCJ2ZXJzaW9uIjoiMS4wIiwic3ViIjoiWkVUVEEiLCJpYXQiOjE2NzU4NzI1MDd9.f3JgVRt7_VrifNWTaRMW3aQfrKbtDbIxlzoenJRYJo0"); - variantAnnotator = VariantAnnotatorFactory.buildVariantAnnotator(storageConfiguration, projectMetadata, options); - results = variantAnnotator.annotate(Collections.singletonList(new Variant("10:113588287:G:A"))); - assertEquals(1, results.size()); - assertTrue(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("clinvar"))); - assertFalse(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("cosmic"))); - assertTrue(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("hgmd"))); - - // Using COSMIC = HGMD token - storageConfiguration.getCellbase().setApiKey("eyJhbGciOiJIUzI1NiJ9.eyJzb3VyY2VzIjp7ImNvc21pYyI6OTIyMzM3MjAzNjg1NDc3NTgwNywiaGdtZCI6OTIyMzM3MjAzNjg1NDc3NTgwN30sInZlcnNpb24iOiIxLjAiLCJzdWIiOiJaRVRUQSIsImlhdCI6MTY3NTg3MjUyN30.NCCFc4SAhjUsN5UU0wXGY6nCZx8jLglvaO1cNZYI0u4"); - variantAnnotator = VariantAnnotatorFactory.buildVariantAnnotator(storageConfiguration, projectMetadata, options); - results = variantAnnotator.annotate(Collections.singletonList(new Variant("10:113588287:G:A"))); - assertEquals(1, results.size()); - assertTrue(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("clinvar"))); - assertTrue(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("cosmic"))); - assertTrue(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("hgmd"))); - } + apiKey = System.getenv("CELLBASE_HGMD_APIKEY"); + if (StringUtils.isNotEmpty(apiKey)) { + storageConfiguration.getCellbase().setApiKey(apiKey); + variantAnnotator = VariantAnnotatorFactory.buildVariantAnnotator(storageConfiguration, projectMetadata, options); + results = variantAnnotator.annotate(Collections.singletonList(new Variant("10:113588287:G:A"))); + assertEquals(1, results.size()); + assertTrue(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("clinvar"))); + assertFalse(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("cosmic"))); + assertTrue(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("hgmd"))); + } - private Set getSources(VariantAnnotation variantAnnotation) { - Set sources = new HashSet<>(); - if (variantAnnotation != null && CollectionUtils.isNotEmpty(variantAnnotation.getTraitAssociation())) { - for (EvidenceEntry entry : variantAnnotation.getTraitAssociation()) { - sources.add(entry.getSource().getName()); - } + // Using COSMIC + HGMD token + apiKey = System.getenv("CELLBASE_COSMIC_HGMD_APIKEY"); + if (StringUtils.isNotEmpty(apiKey)) { + storageConfiguration.getCellbase().setApiKey(apiKey); + variantAnnotator = VariantAnnotatorFactory.buildVariantAnnotator(storageConfiguration, projectMetadata, options); + results = variantAnnotator.annotate(Collections.singletonList(new Variant("10:113588287:G:A"))); + assertEquals(1, results.size()); + assertTrue(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("clinvar"))); + assertTrue(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("cosmic"))); + assertTrue(results.get(0).getTraitAssociation().stream().anyMatch(e -> e.getSource().getName().equals("hgmd"))); } - return sources; } public static class TestCellBaseRestVariantAnnotator extends CellBaseRestVariantAnnotator { From 061730a7e45b5af2230fc9f113f235d18faf5a20 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Tue, 29 Aug 2023 15:26:31 +0100 Subject: [PATCH 089/109] app: Add migration for renaming cellbase.token to cellbase.apiKey #TASK-4898 --- .../catalog/RenameCellBaseToken2ApiKey.java | 50 +++++++++++++++++++ .../config/storage/CellBaseConfiguration.java | 15 ------ 2 files changed, 50 insertions(+), 15 deletions(-) create mode 100644 opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java new file mode 100644 index 00000000000..72fe8e6499e --- /dev/null +++ b/opencga-app/src/main/java/org/opencb/opencga/app/migrations/v2_9_0/catalog/RenameCellBaseToken2ApiKey.java @@ -0,0 +1,50 @@ +package org.opencb.opencga.app.migrations.v2_9_0.catalog; + +import com.mongodb.client.model.Projections; +import com.mongodb.client.model.UpdateOneModel; +import com.mongodb.client.model.Updates; +import org.bson.Document; +import org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptorFactory; +import org.opencb.opencga.catalog.migration.Migration; +import org.opencb.opencga.catalog.migration.MigrationTool; + +import java.util.List; + +import static com.mongodb.client.model.Filters.eq; + +@Migration(id = "rename_cellbase_token_2_api_key" , + description = "Rename CellBase Token to ApiKey", + version = "2.9.0", + domain = Migration.MigrationDomain.CATALOG, + language = Migration.MigrationLanguage.JAVA, + date = 20230829 +) +public class RenameCellBaseToken2ApiKey extends MigrationTool { + + @Override + protected void run() throws Exception { + + migrateCollection(MongoDBAdaptorFactory.USER_COLLECTION, + new Document("projects.id", new Document("$exists", true)), + Projections.include("_id", "projects"), + (userDocument, bulk) -> { + List projects = userDocument.getList("projects", Document.class); + for (int i = 0; i < projects.size(); i++) { + Document project = projects.get(i); + Document cellbase = project.get("cellbase", Document.class); + if (cellbase != null) { + String token = cellbase.getString("token"); + if (token != null) { + bulk.add(new UpdateOneModel<>( + eq("_id", userDocument.get("_id")), + Updates.combine( + Updates.set("projects." + i + ".cellbase.apiKey", token), + Updates.unset("projects." + i + ".cellbase.token") + ))); + } + } + } + }); + } + +} diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/CellBaseConfiguration.java b/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/CellBaseConfiguration.java index 1818beb363c..2ef6a77cca4 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/CellBaseConfiguration.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/config/storage/CellBaseConfiguration.java @@ -42,10 +42,6 @@ public class CellBaseConfiguration { @DataField(id = "dataRelease", description = "CellBase data release version to be used. If empty, will use the active one") private String dataRelease; - @Deprecated - @DataField(id = "token", deprecated = true, description = "CellBase token to access to the licensed/restricted data sources such as COSMIC, HGMD,...") - private String token; - @DataField(id = "apiKey", description = "API key to access to the licensed/restricted data sources (COSMIC, HGMD,...) and to manage quota.") private String apiKey; @@ -62,7 +58,6 @@ public CellBaseConfiguration(String url, String version, String dataRelease, Str this.url = url; this.version = version; this.dataRelease = dataRelease; - this.token = apiKey; this.apiKey = apiKey; } @@ -72,7 +67,6 @@ public String toString() { sb.append("url='").append(url).append('\''); sb.append(", version='").append(version).append('\''); sb.append(", dataRelease='").append(dataRelease).append('\''); - sb.append(", token='").append(token).append('\''); sb.append(", apiKey='").append(apiKey).append('\''); sb.append('}'); return sb.toString(); @@ -105,15 +99,6 @@ public CellBaseConfiguration setDataRelease(String dataRelease) { return this; } -// public String getToken() { -// return apiKey; -// } -// -// public CellBaseConfiguration setToken(String token) { -// this.apiKey = token; -// return this; -// } - public String getApiKey() { return apiKey; } From 88ed0ea4ef071c2257b2fa5e6c3e1422f48cdb49 Mon Sep 17 00:00:00 2001 From: pfurio Date: Wed, 30 Aug 2023 09:40:17 +0200 Subject: [PATCH 090/109] core: improve regex description, #TASK-4906 --- .../main/java/org/opencb/opencga/core/api/ParamConstants.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java b/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java index 6a42182cf34..a34b818924a 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java @@ -38,7 +38,8 @@ public class ParamConstants { public static final String RELEASE_DESCRIPTION = "Release when it was created"; public static final String INTERNAL_STATUS_PARAM = "internalStatus"; public static final String INTERNAL_STATUS_DESCRIPTION = "Filter by internal status"; - private static final String REGEX_SUPPORT = ". Also admits basic regular expressions like '~/^value/i'"; + private static final String REGEX_SUPPORT = ". Also admits basic regular expressions using the operator '~', " + + "i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search."; @Deprecated // Use INTERNAL_VARIANT_INDEX_STATUS_PARAM public static final String INTERNAL_INDEX_STATUS_PARAM = "internalIndexStatus"; public static final String INTERNAL_VARIANT_INDEX_STATUS_PARAM = "internalVariantIndexStatus"; From c34d02549b6d595a38a33591d59beae764b419a2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Wed, 30 Aug 2023 11:38:46 +0100 Subject: [PATCH 091/109] core: Fix cellbase validator to acknowledge tokens. #TASK-4913 --- .../core/cellbase/CellBaseValidator.java | 44 ++++++++++++++++++- .../core/cellbase/CellBaseValidatorTest.java | 35 +++++++++++++++ 2 files changed, 78 insertions(+), 1 deletion(-) diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java b/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java index 21f5c79fecd..43da58f396a 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java @@ -1,6 +1,8 @@ package org.opencb.opencga.core.cellbase; +import io.jsonwebtoken.JwtException; import org.apache.commons.lang3.StringUtils; +import org.opencb.biodata.models.variant.avro.VariantAnnotation; import org.opencb.cellbase.client.rest.CellBaseClient; import org.opencb.cellbase.core.config.SpeciesConfiguration; import org.opencb.cellbase.core.config.SpeciesProperties; @@ -8,6 +10,7 @@ import org.opencb.cellbase.core.result.CellBaseDataResponse; import org.opencb.cellbase.core.token.DataAccessTokenManager; import org.opencb.cellbase.core.token.DataAccessTokenSources; +import org.opencb.commons.datastore.core.QueryOptions; import org.opencb.opencga.core.common.VersionUtils; import org.opencb.opencga.core.config.storage.CellBaseConfiguration; import org.slf4j.Logger; @@ -15,6 +18,7 @@ import java.io.IOException; import java.util.ArrayList; +import java.util.Collections; import java.util.Comparator; import java.util.List; import java.util.stream.Collectors; @@ -46,6 +50,7 @@ private CellBaseClient newCellBaseClient(CellBaseConfiguration cellBaseConfigura toCellBaseSpeciesName(species), assembly, cellBaseConfiguration.getDataRelease(), + cellBaseConfiguration.getToken(), cellBaseConfiguration.toClientConfiguration()); } @@ -136,7 +141,7 @@ public void validate() throws IOException { validate(false); } - public CellBaseConfiguration validate(boolean autoComplete) throws IOException { + private CellBaseConfiguration validate(boolean autoComplete) throws IOException { CellBaseConfiguration cellBaseConfiguration = getCellBaseConfiguration(); String inputVersion = getVersion(); CellBaseDataResponse species; @@ -189,6 +194,38 @@ public CellBaseConfiguration validate(boolean autoComplete) throws IOException { } } } + if (getToken() != null) { + // Check it's supported + if (!supportsToken(serverVersion)) { + throw new IllegalArgumentException("Token not supported for cellbase " + + "url: '" + getURL() + "'" + + ", version: '" + inputVersion + "'"); + } + + // Check it's an actual token + DataAccessTokenManager tokenManager = new DataAccessTokenManager(); + try { + tokenManager.decode(getToken()); + } catch (JwtException e) { + throw new IllegalArgumentException("Malformed token for cellbase " + + "url: '" + getURL() + "'" + + ", version: '" + inputVersion + + "', species: '" + getSpecies() + + "', assembly: '" + getAssembly() + "'"); + } + + // Check it's a valid token + CellBaseDataResponse response = cellBaseClient.getVariantClient() + .getAnnotationByVariantIds(Collections.singletonList("1:1:N:C"), new QueryOptions(), true); + if (response.firstResult() == null) { + throw new IllegalArgumentException("Invalid token for cellbase " + + "url: '" + getURL() + "'" + + ", version: '" + inputVersion + + "', species: '" + getSpecies() + + "', assembly: '" + getAssembly() + "'"); + } + } + return cellBaseConfiguration; } @@ -231,6 +268,11 @@ public static boolean supportsDataReleaseActiveByDefaultIn(String serverVersion) return VersionUtils.isMinVersion("5.5.0", serverVersion, true); } + public static boolean supportsToken(String serverVersion) { + // Tokens support starts at version 5.4.0 + return VersionUtils.isMinVersion("5.4.0", serverVersion); + } + public String getVersionFromServerMajor() throws IOException { return major(getVersionFromServer()); } diff --git a/opencga-core/src/test/java/org/opencb/opencga/core/cellbase/CellBaseValidatorTest.java b/opencga-core/src/test/java/org/opencb/opencga/core/cellbase/CellBaseValidatorTest.java index 36db80985f0..38d91dd0fc8 100644 --- a/opencga-core/src/test/java/org/opencb/opencga/core/cellbase/CellBaseValidatorTest.java +++ b/opencga-core/src/test/java/org/opencb/opencga/core/cellbase/CellBaseValidatorTest.java @@ -1,6 +1,8 @@ package org.opencb.opencga.core.cellbase; +import org.apache.commons.lang3.StringUtils; import org.junit.Assert; +import org.junit.Assume; import org.junit.Rule; import org.junit.Test; import org.junit.rules.ExpectedException; @@ -70,4 +72,37 @@ public void testNoActiveReleases() throws IOException { thrown.expectMessage("No active data releases found on cellbase"); CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.1", null, null), "mmusculus", "GRCm38", true); } + + @Test + public void testToken() throws IOException { + String token = System.getenv("CELLBASE_HGMD_TOKEN"); + Assume.assumeTrue(StringUtils.isNotEmpty(token)); + CellBaseConfiguration validated = CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.4", null, token), "hsapiens", "grch38", true); + Assert.assertNotNull(validated.getToken()); + } + + @Test + public void testTokenNotSupported() throws IOException { + String token = System.getenv("CELLBASE_HGMD_TOKEN"); + Assume.assumeTrue(StringUtils.isNotEmpty(token)); + CellBaseConfiguration validated = CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.1", null, token), "hsapiens", "grch38", true); + Assert.assertNotNull(validated.getToken()); + } + + @Test + public void testMalformedToken() throws IOException { + thrown.expectMessage("Malformed token for cellbase"); + String token = "MALFORMED_TOKEN"; + CellBaseConfiguration validated = CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.4", null, token), "hsapiens", "grch38", true); + Assert.assertNotNull(validated.getToken()); + } + + @Test + public void testUnsignedToken() throws IOException { + thrown.expectMessage("Invalid token for cellbase"); + String token = "eyJhbGciOiJIUzI1NiJ9.eyJzb3VyY2VzIjp7ImhnbWQiOjkyMjMzNzIwMzY4NTQ3NzU4MDd9LCJ2ZXJzaW9uIjoiMS4wIiwic3ViIjoiWkVUVEEiLCJpYXQiOjE2OTMyMTY5MDd9.invalidsignature"; + CellBaseConfiguration validated = CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.4", null, token), "hsapiens", "grch38", true); + Assert.assertNotNull(validated.getToken()); + } + } \ No newline at end of file From 24e51ea1d9848cfa8e32f396412fd3b8058fcc78 Mon Sep 17 00:00:00 2001 From: pfurio Date: Wed, 30 Aug 2023 15:02:16 +0200 Subject: [PATCH 092/109] app: fix client and cli generator, #TASK-4917 --- opencga-app/app/misc/clients/rest_client_generator.py | 3 +++ .../server/generator/writers/ParentClientRestApiWriter.java | 2 ++ 2 files changed, 5 insertions(+) diff --git a/opencga-app/app/misc/clients/rest_client_generator.py b/opencga-app/app/misc/clients/rest_client_generator.py index 8239fa55709..bfb3b78489f 100644 --- a/opencga-app/app/misc/clients/rest_client_generator.py +++ b/opencga-app/app/misc/clients/rest_client_generator.py @@ -198,6 +198,9 @@ def get_method_name(self, endpoint, category): # /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretationId}/merge elif self.all_arg([items[0], items[2]]) and not self.any_arg([items[1], items[3]]): method_name = '_'.join([items[3], items[1]]) + # /{apiVersion}/admin/users/{user}/groups/update + elif self.all_arg([items[1]]) and not self.any_arg([items[0], items[2], items[3]]): + method_name = '_'.join([items[0], items[3], items[2]]) elif len(items) == 5: # e.g. /{apiVersion}/files/{file}/annotationSets/{annotationSet}/annotations/update if self.all_arg([items[0], items[2]]) and not self.any_arg([items[1], items[3], items[4]]): diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/ParentClientRestApiWriter.java b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/ParentClientRestApiWriter.java index 2ac80dfd288..72857bc2aec 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/ParentClientRestApiWriter.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/generator/writers/ParentClientRestApiWriter.java @@ -218,6 +218,8 @@ protected static String getMethodName(String subpath) { // methodName = items[3] + "_" + items[1] + "_" + items[2]; } else if (items[0].contains("}") && items[2].contains("}") && (!items[1].contains("}")) && (!items[3].contains("}"))) { methodName = items[3] + "_" + items[1]; + } else if (items[1].contains("}") && (!items[0].contains("}") && !items[2].contains("}") && !items[3].contains("}"))) { + methodName = items[0] + "_" + items[3] + "_" + items[2]; } } else if (items.length == 5) { if (items[0].contains("}") && items[2].contains("}") && (!items[1].contains("}")) && (!items[3].contains("}")) From 4722e48728dbb6761c4a65643a52c0f339080866 Mon Sep 17 00:00:00 2001 From: pfurio Date: Wed, 30 Aug 2023 15:04:32 +0200 Subject: [PATCH 093/109] app: generate new clients and cli, #TASK-4917 --- .../app/cli/main/OpenCgaCompleter.java | 4 +-- .../app/cli/main/OpencgaCliOptionsParser.java | 3 +- .../main/executors/AdminCommandExecutor.java | 36 +++++++++++++++++++ .../cli/main/options/AdminCommandOptions.java | 28 +++++++++++++++ .../AnalysisVariantCommandOptions.java | 4 +-- opencga-client/src/main/R/R/Admin-methods.R | 13 +++++-- .../src/main/R/R/Alignment-methods.R | 2 +- opencga-client/src/main/R/R/AllGenerics.R | 18 +++++----- .../src/main/R/R/Clinical-methods.R | 4 +-- opencga-client/src/main/R/R/Cohort-methods.R | 4 +-- opencga-client/src/main/R/R/Family-methods.R | 4 +-- opencga-client/src/main/R/R/File-methods.R | 4 +-- opencga-client/src/main/R/R/GA4GH-methods.R | 2 +- .../src/main/R/R/Individual-methods.R | 4 +-- opencga-client/src/main/R/R/Job-methods.R | 4 +-- opencga-client/src/main/R/R/Meta-methods.R | 2 +- .../src/main/R/R/Operation-methods.R | 2 +- opencga-client/src/main/R/R/Panel-methods.R | 2 +- opencga-client/src/main/R/R/Project-methods.R | 2 +- opencga-client/src/main/R/R/Sample-methods.R | 2 +- opencga-client/src/main/R/R/Study-methods.R | 4 +-- opencga-client/src/main/R/R/User-methods.R | 4 +-- opencga-client/src/main/R/R/Variant-methods.R | 2 +- .../client/rest/clients/AdminClient.java | 20 +++++++++-- .../client/rest/clients/AlignmentClient.java | 4 +-- .../rest/clients/ClinicalAnalysisClient.java | 4 +-- .../client/rest/clients/CohortClient.java | 4 +-- .../rest/clients/DiseasePanelClient.java | 4 +-- .../client/rest/clients/FamilyClient.java | 4 +-- .../client/rest/clients/FileClient.java | 4 +-- .../client/rest/clients/GA4GHClient.java | 4 +-- .../client/rest/clients/IndividualClient.java | 4 +-- .../client/rest/clients/JobClient.java | 4 +-- .../client/rest/clients/MetaClient.java | 4 +-- .../client/rest/clients/ProjectClient.java | 4 +-- .../client/rest/clients/SampleClient.java | 4 +-- .../client/rest/clients/StudyClient.java | 4 +-- .../client/rest/clients/UserClient.java | 4 +-- .../client/rest/clients/VariantClient.java | 4 +-- .../rest/clients/VariantOperationClient.java | 4 +-- opencga-client/src/main/javascript/Admin.js | 13 ++++++- .../src/main/javascript/Alignment.js | 2 +- .../src/main/javascript/ClinicalAnalysis.js | 2 +- opencga-client/src/main/javascript/Cohort.js | 2 +- .../src/main/javascript/DiseasePanel.js | 2 +- opencga-client/src/main/javascript/Family.js | 2 +- opencga-client/src/main/javascript/File.js | 2 +- opencga-client/src/main/javascript/GA4GH.js | 2 +- .../src/main/javascript/Individual.js | 2 +- opencga-client/src/main/javascript/Job.js | 2 +- opencga-client/src/main/javascript/Meta.js | 2 +- opencga-client/src/main/javascript/Project.js | 2 +- opencga-client/src/main/javascript/Sample.js | 2 +- opencga-client/src/main/javascript/Study.js | 2 +- opencga-client/src/main/javascript/User.js | 2 +- opencga-client/src/main/javascript/Variant.js | 2 +- .../src/main/javascript/VariantOperation.js | 2 +- .../pyopencga/rest_clients/admin_client.py | 17 +++++++-- .../rest_clients/alignment_client.py | 4 +-- .../rest_clients/clinical_analysis_client.py | 4 +-- .../pyopencga/rest_clients/cohort_client.py | 4 +-- .../rest_clients/disease_panel_client.py | 4 +-- .../pyopencga/rest_clients/family_client.py | 4 +-- .../pyopencga/rest_clients/file_client.py | 4 +-- .../pyopencga/rest_clients/ga4gh_client.py | 4 +-- .../rest_clients/individual_client.py | 4 +-- .../pyopencga/rest_clients/job_client.py | 4 +-- .../pyopencga/rest_clients/meta_client.py | 4 +-- .../pyopencga/rest_clients/project_client.py | 4 +-- .../pyopencga/rest_clients/sample_client.py | 4 +-- .../pyopencga/rest_clients/study_client.py | 4 +-- .../pyopencga/rest_clients/user_client.py | 4 +-- .../pyopencga/rest_clients/variant_client.py | 4 +-- .../rest_clients/variant_operation_client.py | 4 +-- 74 files changed, 239 insertions(+), 125 deletions(-) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java index fa69afab38d..6627d4d82f1 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023-04-18 OpenCB +* Copyright 2015-2023-08-30 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -70,7 +70,7 @@ public abstract class OpenCgaCompleter implements Completer { .map(Candidate::new) .collect(toList()); - private List adminList = asList( "audit-group-by","catalog-index-stats","catalog-install","catalog-jwt","users-create","users-import","users-search","users-sync") + private List adminList = asList( "audit-group-by","catalog-index-stats","catalog-install","catalog-jwt","users-create","users-import","users-search","users-sync","update-groups-users") .stream() .map(Candidate::new) .collect(toList()); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java index c18998aabcc..b619c612c32 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023-04-18 OpenCB +* Copyright 2015-2023-08-30 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. @@ -188,6 +188,7 @@ public OpencgaCliOptionsParser() { adminSubCommands.addCommand("users-import", adminCommandOptions.importUsersCommandOptions); adminSubCommands.addCommand("users-search", adminCommandOptions.searchUsersCommandOptions); adminSubCommands.addCommand("users-sync", adminCommandOptions.syncUsersCommandOptions); + adminSubCommands.addCommand("update-groups-users", adminCommandOptions.usersUpdateGroupsCommandOptions); individualsCommandOptions = new IndividualsCommandOptions(commonCommandOptions, jCommander); jCommander.addCommand("individuals", individualsCommandOptions); diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java index 9ab6c51ed00..a16efb4df47 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AdminCommandExecutor.java @@ -19,11 +19,13 @@ import org.opencb.opencga.app.cli.main.options.AdminCommandOptions; import java.util.Map; +import org.opencb.opencga.catalog.utils.ParamUtils.AddRemoveAction; import org.opencb.opencga.core.models.admin.GroupSyncParams; import org.opencb.opencga.core.models.admin.InstallationParams; import org.opencb.opencga.core.models.admin.JWTParams; import org.opencb.opencga.core.models.admin.UserCreateParams; import org.opencb.opencga.core.models.admin.UserImportParams; +import org.opencb.opencga.core.models.admin.UserUpdateGroup; import org.opencb.opencga.core.models.common.Enums.Resource; import org.opencb.opencga.core.models.sample.Sample; import org.opencb.opencga.core.models.study.Group; @@ -87,6 +89,9 @@ public void execute() throws Exception { case "users-sync": queryResponse = syncUsers(); break; + case "update-groups-users": + queryResponse = usersUpdateGroups(); + break; default: logger.error("Subcommand not valid"); break; @@ -288,4 +293,35 @@ private RestResponse syncUsers() throws Exception { } return openCGAClient.getAdminClient().syncUsers(groupSyncParams); } + + private RestResponse usersUpdateGroups() throws Exception { + logger.debug("Executing usersUpdateGroups in Admin command line"); + + AdminCommandOptions.UsersUpdateGroupsCommandOptions commandOptions = adminCommandOptions.usersUpdateGroupsCommandOptions; + + ObjectMap queryParams = new ObjectMap(); + queryParams.putIfNotNull("action", commandOptions.action); + + + UserUpdateGroup userUpdateGroup = null; + if (commandOptions.jsonDataModel) { + userUpdateGroup = new UserUpdateGroup(); + RestResponse res = new RestResponse<>(); + res.setType(QueryType.VOID); + PrintUtils.println(getObjectAsJSON(userUpdateGroup)); + return res; + } else if (commandOptions.jsonFile != null) { + userUpdateGroup = JacksonUtils.getDefaultObjectMapper() + .readValue(new java.io.File(commandOptions.jsonFile), UserUpdateGroup.class); + } else { + ObjectMap beanParams = new ObjectMap(); + putNestedIfNotNull(beanParams, "studyIds",commandOptions.studyIds, true); + putNestedIfNotNull(beanParams, "groupIds",commandOptions.groupIds, true); + + userUpdateGroup = JacksonUtils.getDefaultObjectMapper().copy() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true) + .readValue(beanParams.toJson(), UserUpdateGroup.class); + } + return openCGAClient.getAdminClient().usersUpdateGroups(commandOptions.user, userUpdateGroup, queryParams); + } } \ No newline at end of file diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AdminCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AdminCommandOptions.java index ae9c1397750..f246d8a36d8 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AdminCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AdminCommandOptions.java @@ -41,6 +41,7 @@ public class AdminCommandOptions { public ImportUsersCommandOptions importUsersCommandOptions; public SearchUsersCommandOptions searchUsersCommandOptions; public SyncUsersCommandOptions syncUsersCommandOptions; + public UsersUpdateGroupsCommandOptions usersUpdateGroupsCommandOptions; public AdminCommandOptions(CommonCommandOptions commonCommandOptions, JCommander jCommander) { @@ -55,6 +56,7 @@ public AdminCommandOptions(CommonCommandOptions commonCommandOptions, JCommander this.importUsersCommandOptions = new ImportUsersCommandOptions(); this.searchUsersCommandOptions = new SearchUsersCommandOptions(); this.syncUsersCommandOptions = new SyncUsersCommandOptions(); + this.usersUpdateGroupsCommandOptions = new UsersUpdateGroupsCommandOptions(); } @@ -278,4 +280,30 @@ public class SyncUsersCommandOptions { } + @Parameters(commandNames = {"update-groups-users"}, commandDescription ="Add or remove users from existing groups") + public class UsersUpdateGroupsCommandOptions { + + @ParametersDelegate + public CommonCommandOptions commonOptions = commonCommandOptions; + + @Parameter(names = {"--json-file"}, description = "File with the body data in JSON format. Note, that using this parameter will ignore all the other parameters.", required = false, arity = 1) + public String jsonFile; + + @Parameter(names = {"--json-data-model"}, description = "Show example of file structure for body data.", help = true, arity = 0) + public Boolean jsonDataModel = false; + + @Parameter(names = {"--user", "-u"}, description = "User ID", required = true, arity = 1) + public String user; + + @Parameter(names = {"--action"}, description = "Action to be performed: ADD or REMOVE user to/from groups", required = false, arity = 1) + public String action = "ADD"; + + @Parameter(names = {"--study-ids"}, description = "The body web service studyIds parameter", required = false, arity = 1) + public String studyIds; + + @Parameter(names = {"--group-ids"}, description = "The body web service groupIds parameter", required = false, arity = 1) + public String groupIds; + + } + } \ No newline at end of file diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java index fc752daaf98..0b37bec1c1c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisVariantCommandOptions.java @@ -925,8 +925,8 @@ public class RunGwasCommandOptions { @Parameter(names = {"--phenotype"}, description = "The body web service phenotype parameter", required = false, arity = 1) public String phenotype; - @Parameter(names = {"--index"}, description = "The body web service index parameter", required = false, arity = 1) - public Boolean index; + @Parameter(names = {"--index"}, description = "The body web service index parameter", required = false, help = true, arity = 0) + public boolean index = false; @Parameter(names = {"--index-score-id"}, description = "The body web service indexScoreId parameter", required = false, arity = 1) public String indexScoreId; diff --git a/opencga-client/src/main/R/R/Admin-methods.R b/opencga-client/src/main/R/R/Admin-methods.R index 11b7d569372..5d46536451d 100644 --- a/opencga-client/src/main/R/R/Admin-methods.R +++ b/opencga-client/src/main/R/R/Admin-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-04-18 +# Autogenerated on: 2023-08-30 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -28,6 +28,7 @@ #' | importUsers | /{apiVersion}/admin/users/import | body[*] | #' | searchUsers | /{apiVersion}/admin/users/search | include, exclude, limit, skip, count, user, account, authenticationId | #' | syncUsers | /{apiVersion}/admin/users/sync | body[*] | +#' | usersUpdateGroups | /{apiVersion}/admin/users/{user}/groups/update | user[*], action, body[*] | #' #' @md #' @seealso \url{http://docs.opencb.org/display/opencga/Using+OpenCGA} and the RESTful API documentation @@ -35,7 +36,7 @@ #' [*]: Required parameter #' @export -setMethod("adminClient", "OpencgaR", function(OpencgaR, endpointName, params=NULL, ...) { +setMethod("adminClient", "OpencgaR", function(OpencgaR, user, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/admin/audit/groupBy: @@ -100,5 +101,13 @@ setMethod("adminClient", "OpencgaR", function(OpencgaR, endpointName, params=NUL #' @param data JSON containing the parameters. syncUsers=fetchOpenCGA(object=OpencgaR, category="admin", categoryId=NULL, subcategory="users", subcategoryId=NULL, action="sync", params=params, httpMethod="POST", as.queryParam=NULL, ...), + + #' @section Endpoint /{apiVersion}/admin/users/{user}/groups/update: + #' Add or remove users from existing groups. + #' @param user User ID. + #' @param action Action to be performed: ADD or REMOVE user to/from groups. Allowed values: ['ADD REMOVE'] + #' @param data JSON containing the parameters. + usersUpdateGroups=fetchOpenCGA(object=OpencgaR, category="admin/users", categoryId=user, subcategory="groups", + subcategoryId=NULL, action="update", params=params, httpMethod="POST", as.queryParam=NULL, ...), ) }) \ No newline at end of file diff --git a/opencga-client/src/main/R/R/Alignment-methods.R b/opencga-client/src/main/R/R/Alignment-methods.R index 00be80c77b7..206b0aa2646 100644 --- a/opencga-client/src/main/R/R/Alignment-methods.R +++ b/opencga-client/src/main/R/R/Alignment-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-04-18 +# Autogenerated on: 2023-08-30 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/AllGenerics.R b/opencga-client/src/main/R/R/AllGenerics.R index 7c9d2230cf6..8e9baedd284 100644 --- a/opencga-client/src/main/R/R/AllGenerics.R +++ b/opencga-client/src/main/R/R/AllGenerics.R @@ -1,6 +1,6 @@ # ############################################################################## ## UserClient -setGeneric("userClient", function(OpencgaR, filterId, users, user, endpointName, params=NULL, ...) +setGeneric("userClient", function(OpencgaR, user, filterId, users, endpointName, params=NULL, ...) standardGeneric("userClient")) # ############################################################################## @@ -10,17 +10,17 @@ setGeneric("projectClient", function(OpencgaR, projects, project, endpointName, # ############################################################################## ## StudyClient -setGeneric("studyClient", function(OpencgaR, members, templateId, studies, variableSet, group, study, endpointName, params=NULL, ...) +setGeneric("studyClient", function(OpencgaR, members, variableSet, studies, group, study, templateId, endpointName, params=NULL, ...) standardGeneric("studyClient")) # ############################################################################## ## FileClient -setGeneric("fileClient", function(OpencgaR, folder, file, members, files, annotationSet, endpointName, params=NULL, ...) +setGeneric("fileClient", function(OpencgaR, files, members, file, annotationSet, folder, endpointName, params=NULL, ...) standardGeneric("fileClient")) # ############################################################################## ## JobClient -setGeneric("jobClient", function(OpencgaR, members, jobs, job, endpointName, params=NULL, ...) +setGeneric("jobClient", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...) standardGeneric("jobClient")) # ############################################################################## @@ -30,17 +30,17 @@ setGeneric("sampleClient", function(OpencgaR, members, sample, samples, annotati # ############################################################################## ## IndividualClient -setGeneric("individualClient", function(OpencgaR, members, individual, annotationSet, individuals, endpointName, params=NULL, ...) +setGeneric("individualClient", function(OpencgaR, members, individuals, annotationSet, individual, endpointName, params=NULL, ...) standardGeneric("individualClient")) # ############################################################################## ## FamilyClient -setGeneric("familyClient", function(OpencgaR, members, families, family, annotationSet, endpointName, params=NULL, ...) +setGeneric("familyClient", function(OpencgaR, members, family, annotationSet, families, endpointName, params=NULL, ...) standardGeneric("familyClient")) # ############################################################################## ## CohortClient -setGeneric("cohortClient", function(OpencgaR, members, cohort, annotationSet, cohorts, endpointName, params=NULL, ...) +setGeneric("cohortClient", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) standardGeneric("cohortClient")) # ############################################################################## @@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## ClinicalClient -setGeneric("clinicalClient", function(OpencgaR, clinicalAnalysis, members, interpretation, clinicalAnalyses, interpretations, endpointName, params=NULL, ...) +setGeneric("clinicalClient", function(OpencgaR, interpretations, members, interpretation, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...) standardGeneric("clinicalClient")) # ############################################################################## @@ -80,6 +80,6 @@ setGeneric("ga4ghClient", function(OpencgaR, file, study, endpointName, params=N # ############################################################################## ## AdminClient -setGeneric("adminClient", function(OpencgaR, endpointName, params=NULL, ...) +setGeneric("adminClient", function(OpencgaR, user, endpointName, params=NULL, ...) standardGeneric("adminClient")) diff --git a/opencga-client/src/main/R/R/Clinical-methods.R b/opencga-client/src/main/R/R/Clinical-methods.R index c590dab0b25..f0652ba64dd 100644 --- a/opencga-client/src/main/R/R/Clinical-methods.R +++ b/opencga-client/src/main/R/R/Clinical-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-04-18 +# Autogenerated on: 2023-08-30 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -58,7 +58,7 @@ #' [*]: Required parameter #' @export -setMethod("clinicalClient", "OpencgaR", function(OpencgaR, clinicalAnalysis, members, interpretation, clinicalAnalyses, interpretations, endpointName, params=NULL, ...) { +setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, members, interpretation, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R index 3d1c6034484..2bcb87bbbbc 100644 --- a/opencga-client/src/main/R/R/Cohort-methods.R +++ b/opencga-client/src/main/R/R/Cohort-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-04-18 +# Autogenerated on: 2023-08-30 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("cohortClient", "OpencgaR", function(OpencgaR, members, cohort, annotationSet, cohorts, endpointName, params=NULL, ...) { +setMethod("cohortClient", "OpencgaR", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Family-methods.R b/opencga-client/src/main/R/R/Family-methods.R index b4bdd82fbc5..5993bbe8de9 100644 --- a/opencga-client/src/main/R/R/Family-methods.R +++ b/opencga-client/src/main/R/R/Family-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-04-18 +# Autogenerated on: 2023-08-30 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("familyClient", "OpencgaR", function(OpencgaR, members, families, family, annotationSet, endpointName, params=NULL, ...) { +setMethod("familyClient", "OpencgaR", function(OpencgaR, members, family, annotationSet, families, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/families/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/File-methods.R b/opencga-client/src/main/R/R/File-methods.R index d97412f4788..0ef0d2c83d8 100644 --- a/opencga-client/src/main/R/R/File-methods.R +++ b/opencga-client/src/main/R/R/File-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-04-18 +# Autogenerated on: 2023-08-30 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -54,7 +54,7 @@ #' [*]: Required parameter #' @export -setMethod("fileClient", "OpencgaR", function(OpencgaR, folder, file, members, files, annotationSet, endpointName, params=NULL, ...) { +setMethod("fileClient", "OpencgaR", function(OpencgaR, files, members, file, annotationSet, folder, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/files/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/GA4GH-methods.R b/opencga-client/src/main/R/R/GA4GH-methods.R index defcc45b18f..534e75260ad 100644 --- a/opencga-client/src/main/R/R/GA4GH-methods.R +++ b/opencga-client/src/main/R/R/GA4GH-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-04-18 +# Autogenerated on: 2023-08-30 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Individual-methods.R b/opencga-client/src/main/R/R/Individual-methods.R index 1ded4cea574..019acd410c2 100644 --- a/opencga-client/src/main/R/R/Individual-methods.R +++ b/opencga-client/src/main/R/R/Individual-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-04-18 +# Autogenerated on: 2023-08-30 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("individualClient", "OpencgaR", function(OpencgaR, members, individual, annotationSet, individuals, endpointName, params=NULL, ...) { +setMethod("individualClient", "OpencgaR", function(OpencgaR, members, individuals, annotationSet, individual, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/individuals/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Job-methods.R b/opencga-client/src/main/R/R/Job-methods.R index 9a6319a293c..f85fe4840f7 100644 --- a/opencga-client/src/main/R/R/Job-methods.R +++ b/opencga-client/src/main/R/R/Job-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-04-18 +# Autogenerated on: 2023-08-30 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -40,7 +40,7 @@ #' [*]: Required parameter #' @export -setMethod("jobClient", "OpencgaR", function(OpencgaR, members, jobs, job, endpointName, params=NULL, ...) { +setMethod("jobClient", "OpencgaR", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/jobs/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Meta-methods.R b/opencga-client/src/main/R/R/Meta-methods.R index cfd47fb4f17..d4de1c866b8 100644 --- a/opencga-client/src/main/R/R/Meta-methods.R +++ b/opencga-client/src/main/R/R/Meta-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-04-18 +# Autogenerated on: 2023-08-30 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Operation-methods.R b/opencga-client/src/main/R/R/Operation-methods.R index 8869d0ff5a3..902a0403f47 100644 --- a/opencga-client/src/main/R/R/Operation-methods.R +++ b/opencga-client/src/main/R/R/Operation-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-04-18 +# Autogenerated on: 2023-08-30 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Panel-methods.R b/opencga-client/src/main/R/R/Panel-methods.R index ea88beb1bfa..e7d661d3a2c 100644 --- a/opencga-client/src/main/R/R/Panel-methods.R +++ b/opencga-client/src/main/R/R/Panel-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-04-18 +# Autogenerated on: 2023-08-30 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Project-methods.R b/opencga-client/src/main/R/R/Project-methods.R index 88420d4beb6..b4ab8a5b98e 100644 --- a/opencga-client/src/main/R/R/Project-methods.R +++ b/opencga-client/src/main/R/R/Project-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-04-18 +# Autogenerated on: 2023-08-30 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Sample-methods.R b/opencga-client/src/main/R/R/Sample-methods.R index fa8bc1e707a..89b2d7b5876 100644 --- a/opencga-client/src/main/R/R/Sample-methods.R +++ b/opencga-client/src/main/R/R/Sample-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-04-18 +# Autogenerated on: 2023-08-30 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Study-methods.R b/opencga-client/src/main/R/R/Study-methods.R index 425059d2d03..754fa677dea 100644 --- a/opencga-client/src/main/R/R/Study-methods.R +++ b/opencga-client/src/main/R/R/Study-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-04-18 +# Autogenerated on: 2023-08-30 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -46,7 +46,7 @@ #' [*]: Required parameter #' @export -setMethod("studyClient", "OpencgaR", function(OpencgaR, members, templateId, studies, variableSet, group, study, endpointName, params=NULL, ...) { +setMethod("studyClient", "OpencgaR", function(OpencgaR, members, variableSet, studies, group, study, templateId, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/studies/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/User-methods.R b/opencga-client/src/main/R/R/User-methods.R index 9faadad0488..7fb54a32ff1 100644 --- a/opencga-client/src/main/R/R/User-methods.R +++ b/opencga-client/src/main/R/R/User-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-04-18 +# Autogenerated on: 2023-08-30 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("userClient", "OpencgaR", function(OpencgaR, filterId, users, user, endpointName, params=NULL, ...) { +setMethod("userClient", "OpencgaR", function(OpencgaR, user, filterId, users, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/users/login: diff --git a/opencga-client/src/main/R/R/Variant-methods.R b/opencga-client/src/main/R/R/Variant-methods.R index e9e2f67edeb..0b7a706cb8f 100644 --- a/opencga-client/src/main/R/R/Variant-methods.R +++ b/opencga-client/src/main/R/R/Variant-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-04-18 +# Autogenerated on: 2023-08-30 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java index 4baf9a8229e..2a375bb7b83 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java @@ -25,6 +25,7 @@ import org.opencb.opencga.core.models.admin.JWTParams; import org.opencb.opencga.core.models.admin.UserCreateParams; import org.opencb.opencga.core.models.admin.UserImportParams; +import org.opencb.opencga.core.models.admin.UserUpdateGroup; import org.opencb.opencga.core.models.sample.Sample; import org.opencb.opencga.core.models.study.Group; import org.opencb.opencga.core.models.user.User; @@ -35,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-04-18 +* Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -44,7 +45,7 @@ /** * This class contains methods for the Admin webservices. - * Client version: 2.8.0-SNAPSHOT + * Client version: 2.11.0-SNAPSHOT * PATH: admin */ public class AdminClient extends AbstractParentClient { @@ -165,4 +166,19 @@ public RestResponse syncUsers(GroupSyncParams data) throws ClientExceptio params.put("body", data); return execute("admin", null, "users", null, "sync", params, POST, Group.class); } + + /** + * Add or remove users from existing groups. + * @param user User ID. + * @param data JSON containing the parameters. + * @param params Map containing any of the following optional parameters. + * action: Action to be performed: ADD or REMOVE user to/from groups. + * @return a RestResponse object. + * @throws ClientException ClientException if there is any server error. + */ + public RestResponse usersUpdateGroups(String user, UserUpdateGroup data, ObjectMap params) throws ClientException { + params = params != null ? params : new ObjectMap(); + params.put("body", data); + return execute("admin/users", user, "groups", null, "update", params, POST, Group.class); + } } diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java index c153146ca4e..08257cc1a1a 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java @@ -40,7 +40,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-04-18 +* Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -49,7 +49,7 @@ /** * This class contains methods for the Alignment webservices. - * Client version: 2.8.0-SNAPSHOT + * Client version: 2.11.0-SNAPSHOT * PATH: analysis/alignment */ public class AlignmentClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java index 9da4bc7e24c..32ab712003e 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java @@ -51,7 +51,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-04-18 +* Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -60,7 +60,7 @@ /** * This class contains methods for the ClinicalAnalysis webservices. - * Client version: 2.8.0-SNAPSHOT + * Client version: 2.11.0-SNAPSHOT * PATH: analysis/clinical */ public class ClinicalAnalysisClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java index 11bfc04c972..547601b9329 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java @@ -37,7 +37,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-04-18 +* Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -46,7 +46,7 @@ /** * This class contains methods for the Cohort webservices. - * Client version: 2.8.0-SNAPSHOT + * Client version: 2.11.0-SNAPSHOT * PATH: cohorts */ public class CohortClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java index fc47e555d99..ad5ea1a7047 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java @@ -35,7 +35,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-04-18 +* Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -44,7 +44,7 @@ /** * This class contains methods for the DiseasePanel webservices. - * Client version: 2.8.0-SNAPSHOT + * Client version: 2.11.0-SNAPSHOT * PATH: panels */ public class DiseasePanelClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java index 072933ac1e2..d113cbdaf09 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-04-18 +* Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -45,7 +45,7 @@ /** * This class contains methods for the Family webservices. - * Client version: 2.8.0-SNAPSHOT + * Client version: 2.11.0-SNAPSHOT * PATH: families */ public class FamilyClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java index 553e0983a27..72be6ed305b 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java @@ -43,7 +43,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-04-18 +* Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -52,7 +52,7 @@ /** * This class contains methods for the File webservices. - * Client version: 2.8.0-SNAPSHOT + * Client version: 2.11.0-SNAPSHOT * PATH: files */ public class FileClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java index a4bc5b7f11c..fbb84f972a4 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java @@ -27,7 +27,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-04-18 +* Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -36,7 +36,7 @@ /** * This class contains methods for the GA4GH webservices. - * Client version: 2.8.0-SNAPSHOT + * Client version: 2.11.0-SNAPSHOT * PATH: ga4gh */ public class GA4GHClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java index 3b41baf7ae6..5803d125e54 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-04-18 +* Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -45,7 +45,7 @@ /** * This class contains methods for the Individual webservices. - * Client version: 2.8.0-SNAPSHOT + * Client version: 2.11.0-SNAPSHOT * PATH: individuals */ public class IndividualClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java index 334c154ae53..27245d4011c 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java @@ -37,7 +37,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-04-18 +* Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -46,7 +46,7 @@ /** * This class contains methods for the Job webservices. - * Client version: 2.8.0-SNAPSHOT + * Client version: 2.11.0-SNAPSHOT * PATH: jobs */ public class JobClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java index ac4c311a0bb..c2c015b670d 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java @@ -28,7 +28,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-04-18 +* Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -37,7 +37,7 @@ /** * This class contains methods for the Meta webservices. - * Client version: 2.8.0-SNAPSHOT + * Client version: 2.11.0-SNAPSHOT * PATH: meta */ public class MetaClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java index 9a3094cb554..47aeec33622 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java @@ -32,7 +32,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-04-18 +* Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -41,7 +41,7 @@ /** * This class contains methods for the Project webservices. - * Client version: 2.8.0-SNAPSHOT + * Client version: 2.11.0-SNAPSHOT * PATH: projects */ public class ProjectClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java index efeca3bd4b3..d2dd71bc2f3 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-04-18 +* Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -45,7 +45,7 @@ /** * This class contains methods for the Sample webservices. - * Client version: 2.8.0-SNAPSHOT + * Client version: 2.11.0-SNAPSHOT * PATH: samples */ public class SampleClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java index 47f1ce2dbc9..53502e91c7e 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java @@ -45,7 +45,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-04-18 +* Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -54,7 +54,7 @@ /** * This class contains methods for the Study webservices. - * Client version: 2.8.0-SNAPSHOT + * Client version: 2.11.0-SNAPSHOT * PATH: studies */ public class StudyClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java index bdf3eb4f232..eda89cb9228 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-04-18 +* Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -45,7 +45,7 @@ /** * This class contains methods for the User webservices. - * Client version: 2.8.0-SNAPSHOT + * Client version: 2.11.0-SNAPSHOT * PATH: users */ public class UserClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java index 5b135d4d38e..0d25391978a 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java @@ -62,7 +62,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-04-18 +* Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -71,7 +71,7 @@ /** * This class contains methods for the Variant webservices. - * Client version: 2.8.0-SNAPSHOT + * Client version: 2.11.0-SNAPSHOT * PATH: analysis/variant */ public class VariantClient extends AbstractParentClient { diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java index e15498be36d..ae6bef9d18d 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java @@ -50,7 +50,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-04-18 +* Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -59,7 +59,7 @@ /** * This class contains methods for the VariantOperation webservices. - * Client version: 2.8.0-SNAPSHOT + * Client version: 2.11.0-SNAPSHOT * PATH: operation */ public class VariantOperationClient extends AbstractParentClient { diff --git a/opencga-client/src/main/javascript/Admin.js b/opencga-client/src/main/javascript/Admin.js index 53c4f4e9c41..26d6d454012 100644 --- a/opencga-client/src/main/javascript/Admin.js +++ b/opencga-client/src/main/javascript/Admin.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-04-18 + * Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -116,4 +116,15 @@ export default class Admin extends OpenCGAParentClass { return this._post("admin", null, "users", null, "sync", data); } + /** Add or remove users from existing groups + * @param {String} user - User ID. + * @param {Object} data - JSON containing the parameters. + * @param {Object} [params] - The Object containing the following optional parameters: + * @param {"ADD REMOVE"} [params.action = "ADD"] - Action to be performed: ADD or REMOVE user to/from groups. The default value is ADD. + * @returns {Promise} Promise object in the form of RestResponse instance. + */ + usersUpdateGroups(user, data, params) { + return this._post("admin/users", user, "groups", null, "update", data, params); + } + } \ No newline at end of file diff --git a/opencga-client/src/main/javascript/Alignment.js b/opencga-client/src/main/javascript/Alignment.js index bc3b7eb2c02..33aa92db017 100644 --- a/opencga-client/src/main/javascript/Alignment.js +++ b/opencga-client/src/main/javascript/Alignment.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-04-18 + * Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/ClinicalAnalysis.js b/opencga-client/src/main/javascript/ClinicalAnalysis.js index 30c195691ca..4434d811346 100644 --- a/opencga-client/src/main/javascript/ClinicalAnalysis.js +++ b/opencga-client/src/main/javascript/ClinicalAnalysis.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-04-18 + * Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Cohort.js b/opencga-client/src/main/javascript/Cohort.js index 56f11ab10fa..cb53c5278a3 100644 --- a/opencga-client/src/main/javascript/Cohort.js +++ b/opencga-client/src/main/javascript/Cohort.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-04-18 + * Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/DiseasePanel.js b/opencga-client/src/main/javascript/DiseasePanel.js index c8a18d38ab6..a4bc253c0bd 100644 --- a/opencga-client/src/main/javascript/DiseasePanel.js +++ b/opencga-client/src/main/javascript/DiseasePanel.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-04-18 + * Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Family.js b/opencga-client/src/main/javascript/Family.js index eef6b77e11e..e971b3b2e81 100644 --- a/opencga-client/src/main/javascript/Family.js +++ b/opencga-client/src/main/javascript/Family.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-04-18 + * Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/File.js b/opencga-client/src/main/javascript/File.js index 66ca23ddf1e..b3219c4f08a 100644 --- a/opencga-client/src/main/javascript/File.js +++ b/opencga-client/src/main/javascript/File.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-04-18 + * Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/GA4GH.js b/opencga-client/src/main/javascript/GA4GH.js index e6fb38143ac..ec01beb21de 100644 --- a/opencga-client/src/main/javascript/GA4GH.js +++ b/opencga-client/src/main/javascript/GA4GH.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-04-18 + * Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Individual.js b/opencga-client/src/main/javascript/Individual.js index 2487febccf8..71eb45dbafd 100644 --- a/opencga-client/src/main/javascript/Individual.js +++ b/opencga-client/src/main/javascript/Individual.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-04-18 + * Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Job.js b/opencga-client/src/main/javascript/Job.js index e76d111f0b5..1e1cc91bc52 100644 --- a/opencga-client/src/main/javascript/Job.js +++ b/opencga-client/src/main/javascript/Job.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-04-18 + * Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Meta.js b/opencga-client/src/main/javascript/Meta.js index b0208dd1cfd..24dfe87c63d 100644 --- a/opencga-client/src/main/javascript/Meta.js +++ b/opencga-client/src/main/javascript/Meta.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-04-18 + * Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Project.js b/opencga-client/src/main/javascript/Project.js index 06abda04b57..e240c25cb46 100644 --- a/opencga-client/src/main/javascript/Project.js +++ b/opencga-client/src/main/javascript/Project.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-04-18 + * Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Sample.js b/opencga-client/src/main/javascript/Sample.js index 2c4fdd8956a..03c6a5b8d8f 100644 --- a/opencga-client/src/main/javascript/Sample.js +++ b/opencga-client/src/main/javascript/Sample.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-04-18 + * Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Study.js b/opencga-client/src/main/javascript/Study.js index 029d4133c82..e99e8c7606b 100644 --- a/opencga-client/src/main/javascript/Study.js +++ b/opencga-client/src/main/javascript/Study.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-04-18 + * Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/User.js b/opencga-client/src/main/javascript/User.js index fd3b9adaf52..bfed2a7bfec 100644 --- a/opencga-client/src/main/javascript/User.js +++ b/opencga-client/src/main/javascript/User.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-04-18 + * Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Variant.js b/opencga-client/src/main/javascript/Variant.js index f5f8b2e09a1..ae9365d5448 100644 --- a/opencga-client/src/main/javascript/Variant.js +++ b/opencga-client/src/main/javascript/Variant.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-04-18 + * Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/VariantOperation.js b/opencga-client/src/main/javascript/VariantOperation.js index 604e09d9ccf..f9837f69e25 100644 --- a/opencga-client/src/main/javascript/VariantOperation.js +++ b/opencga-client/src/main/javascript/VariantOperation.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-04-18 + * Autogenerated on: 2023-08-30 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py index 7048467edf6..e982694d126 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-04-18 + Autogenerated on: 2023-08-30 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Admin(_ParentRestClient): """ This class contains methods for the 'Admin' webservices - Client version: 2.8.0-SNAPSHOT + Client version: 2.11.0-SNAPSHOT PATH: /{apiVersion}/admin """ @@ -128,3 +128,16 @@ def sync_users(self, data=None, **options): return self._post(category='admin', resource='sync', subcategory='users', data=data, **options) + def users_update_groups(self, user, data=None, **options): + """ + Add or remove users from existing groups. + PATH: /{apiVersion}/admin/users/{user}/groups/update + + :param dict data: JSON containing the parameters. (REQUIRED) + :param str user: User ID. (REQUIRED) + :param str action: Action to be performed: ADD or REMOVE user to/from + groups. Allowed values: ['ADD REMOVE'] + """ + + return self._post(category='admin/users', resource='update', query_id=user, subcategory='groups', data=data, **options) + diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py index 826ae8b6957..b94f350449a 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-04-18 + Autogenerated on: 2023-08-30 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Alignment(_ParentRestClient): """ This class contains methods for the 'Analysis - Alignment' webservices - Client version: 2.8.0-SNAPSHOT + Client version: 2.11.0-SNAPSHOT PATH: /{apiVersion}/analysis/alignment """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py index e6ced9ecbf3..ca4e1438978 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-04-18 + Autogenerated on: 2023-08-30 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class ClinicalAnalysis(_ParentRestClient): """ This class contains methods for the 'Analysis - Clinical' webservices - Client version: 2.8.0-SNAPSHOT + Client version: 2.11.0-SNAPSHOT PATH: /{apiVersion}/analysis/clinical """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py index 6c685b9772a..fef4cafa48d 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-04-18 + Autogenerated on: 2023-08-30 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Cohort(_ParentRestClient): """ This class contains methods for the 'Cohorts' webservices - Client version: 2.8.0-SNAPSHOT + Client version: 2.11.0-SNAPSHOT PATH: /{apiVersion}/cohorts """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py index 4ec0b95c8fa..8382900c307 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-04-18 + Autogenerated on: 2023-08-30 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class DiseasePanel(_ParentRestClient): """ This class contains methods for the 'Disease Panels' webservices - Client version: 2.8.0-SNAPSHOT + Client version: 2.11.0-SNAPSHOT PATH: /{apiVersion}/panels """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py index ab94612b324..0637f728a08 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-04-18 + Autogenerated on: 2023-08-30 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Family(_ParentRestClient): """ This class contains methods for the 'Families' webservices - Client version: 2.8.0-SNAPSHOT + Client version: 2.11.0-SNAPSHOT PATH: /{apiVersion}/families """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py index 0db45804764..816cdf83c0b 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-04-18 + Autogenerated on: 2023-08-30 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class File(_ParentRestClient): """ This class contains methods for the 'Files' webservices - Client version: 2.8.0-SNAPSHOT + Client version: 2.11.0-SNAPSHOT PATH: /{apiVersion}/files """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py index 0b1c0df4afa..6f62ec62786 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-04-18 + Autogenerated on: 2023-08-30 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class GA4GH(_ParentRestClient): """ This class contains methods for the 'GA4GH' webservices - Client version: 2.8.0-SNAPSHOT + Client version: 2.11.0-SNAPSHOT PATH: /{apiVersion}/ga4gh """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py index e4830dbe5ab..3982f010208 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-04-18 + Autogenerated on: 2023-08-30 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Individual(_ParentRestClient): """ This class contains methods for the 'Individuals' webservices - Client version: 2.8.0-SNAPSHOT + Client version: 2.11.0-SNAPSHOT PATH: /{apiVersion}/individuals """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py index fe0a9ec74d3..313cf0df796 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-04-18 + Autogenerated on: 2023-08-30 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Job(_ParentRestClient): """ This class contains methods for the 'Jobs' webservices - Client version: 2.8.0-SNAPSHOT + Client version: 2.11.0-SNAPSHOT PATH: /{apiVersion}/jobs """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py index 96982cc0e3d..189a5ab62ea 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-04-18 + Autogenerated on: 2023-08-30 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Meta(_ParentRestClient): """ This class contains methods for the 'Meta' webservices - Client version: 2.8.0-SNAPSHOT + Client version: 2.11.0-SNAPSHOT PATH: /{apiVersion}/meta """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py index d28ecf4d846..0784b20594c 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-04-18 + Autogenerated on: 2023-08-30 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Project(_ParentRestClient): """ This class contains methods for the 'Projects' webservices - Client version: 2.8.0-SNAPSHOT + Client version: 2.11.0-SNAPSHOT PATH: /{apiVersion}/projects """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py index dca81d4e863..258189685ef 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-04-18 + Autogenerated on: 2023-08-30 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Sample(_ParentRestClient): """ This class contains methods for the 'Samples' webservices - Client version: 2.8.0-SNAPSHOT + Client version: 2.11.0-SNAPSHOT PATH: /{apiVersion}/samples """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py index 53849f904d7..3726c1e0a3a 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-04-18 + Autogenerated on: 2023-08-30 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Study(_ParentRestClient): """ This class contains methods for the 'Studies' webservices - Client version: 2.8.0-SNAPSHOT + Client version: 2.11.0-SNAPSHOT PATH: /{apiVersion}/studies """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py index 0a446be7d9a..80ac433566b 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-04-18 + Autogenerated on: 2023-08-30 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class User(_ParentRestClient): """ This class contains methods for the 'Users' webservices - Client version: 2.8.0-SNAPSHOT + Client version: 2.11.0-SNAPSHOT PATH: /{apiVersion}/users """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py index cc233157566..32dfa804648 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-04-18 + Autogenerated on: 2023-08-30 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class Variant(_ParentRestClient): """ This class contains methods for the 'Analysis - Variant' webservices - Client version: 2.8.0-SNAPSHOT + Client version: 2.11.0-SNAPSHOT PATH: /{apiVersion}/analysis/variant """ diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py index 80eb4b8c973..4070484d219 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-04-18 + Autogenerated on: 2023-08-30 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -14,7 +14,7 @@ class VariantOperation(_ParentRestClient): """ This class contains methods for the 'Operations - Variant Storage' webservices - Client version: 2.8.0-SNAPSHOT + Client version: 2.11.0-SNAPSHOT PATH: /{apiVersion}/operation """ From af38b8bd620c9b0dce5c7f885d08fcb34fbdcf62 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?= Date: Thu, 31 Aug 2023 16:23:38 +0200 Subject: [PATCH 094/109] client: generate OpenCGA clients to take into account the parameter API key, #TASK-4898, #TASK-4641 --- .../app/cli/main/OpenCgaCompleter.java | 2 +- .../app/cli/main/OpencgaCliOptionsParser.java | 2 +- ...erationsVariantStorageCommandExecutor.java | 2 +- .../executors/ProjectsCommandExecutor.java | 2 +- ...perationsVariantStorageCommandOptions.java | 4 ++-- .../main/options/ProjectsCommandOptions.java | 4 ++-- opencga-client/src/main/R/R/Admin-methods.R | 2 +- .../src/main/R/R/Alignment-methods.R | 2 +- opencga-client/src/main/R/R/AllGenerics.R | 20 +++++++++---------- .../src/main/R/R/Clinical-methods.R | 4 ++-- opencga-client/src/main/R/R/Cohort-methods.R | 4 ++-- opencga-client/src/main/R/R/Family-methods.R | 4 ++-- opencga-client/src/main/R/R/File-methods.R | 4 ++-- opencga-client/src/main/R/R/GA4GH-methods.R | 4 ++-- .../src/main/R/R/Individual-methods.R | 2 +- opencga-client/src/main/R/R/Job-methods.R | 4 ++-- opencga-client/src/main/R/R/Meta-methods.R | 2 +- .../src/main/R/R/Operation-methods.R | 2 +- opencga-client/src/main/R/R/Panel-methods.R | 2 +- opencga-client/src/main/R/R/Project-methods.R | 4 ++-- opencga-client/src/main/R/R/Sample-methods.R | 4 ++-- opencga-client/src/main/R/R/Study-methods.R | 4 ++-- opencga-client/src/main/R/R/User-methods.R | 4 ++-- opencga-client/src/main/R/R/Variant-methods.R | 2 +- .../client/rest/clients/AdminClient.java | 2 +- .../client/rest/clients/AlignmentClient.java | 2 +- .../rest/clients/ClinicalAnalysisClient.java | 2 +- .../client/rest/clients/CohortClient.java | 2 +- .../rest/clients/DiseasePanelClient.java | 2 +- .../client/rest/clients/FamilyClient.java | 2 +- .../client/rest/clients/FileClient.java | 2 +- .../client/rest/clients/GA4GHClient.java | 2 +- .../client/rest/clients/IndividualClient.java | 2 +- .../client/rest/clients/JobClient.java | 2 +- .../client/rest/clients/MetaClient.java | 2 +- .../client/rest/clients/ProjectClient.java | 2 +- .../client/rest/clients/SampleClient.java | 2 +- .../client/rest/clients/StudyClient.java | 2 +- .../client/rest/clients/UserClient.java | 2 +- .../client/rest/clients/VariantClient.java | 2 +- .../rest/clients/VariantOperationClient.java | 2 +- opencga-client/src/main/javascript/Admin.js | 2 +- .../src/main/javascript/Alignment.js | 2 +- .../src/main/javascript/ClinicalAnalysis.js | 2 +- opencga-client/src/main/javascript/Cohort.js | 2 +- .../src/main/javascript/DiseasePanel.js | 2 +- opencga-client/src/main/javascript/Family.js | 2 +- opencga-client/src/main/javascript/File.js | 2 +- opencga-client/src/main/javascript/GA4GH.js | 2 +- .../src/main/javascript/Individual.js | 2 +- opencga-client/src/main/javascript/Job.js | 2 +- opencga-client/src/main/javascript/Meta.js | 2 +- opencga-client/src/main/javascript/Project.js | 2 +- opencga-client/src/main/javascript/Sample.js | 2 +- opencga-client/src/main/javascript/Study.js | 2 +- opencga-client/src/main/javascript/User.js | 2 +- opencga-client/src/main/javascript/Variant.js | 2 +- .../src/main/javascript/VariantOperation.js | 2 +- .../pyopencga/rest_clients/admin_client.py | 2 +- .../rest_clients/alignment_client.py | 2 +- .../rest_clients/clinical_analysis_client.py | 2 +- .../pyopencga/rest_clients/cohort_client.py | 2 +- .../rest_clients/disease_panel_client.py | 2 +- .../pyopencga/rest_clients/family_client.py | 2 +- .../pyopencga/rest_clients/file_client.py | 2 +- .../pyopencga/rest_clients/ga4gh_client.py | 2 +- .../rest_clients/individual_client.py | 2 +- .../pyopencga/rest_clients/job_client.py | 2 +- .../pyopencga/rest_clients/meta_client.py | 2 +- .../pyopencga/rest_clients/project_client.py | 2 +- .../pyopencga/rest_clients/sample_client.py | 2 +- .../pyopencga/rest_clients/study_client.py | 2 +- .../pyopencga/rest_clients/user_client.py | 2 +- .../pyopencga/rest_clients/variant_client.py | 2 +- .../rest_clients/variant_operation_client.py | 2 +- 75 files changed, 96 insertions(+), 96 deletions(-) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java index 6627d4d82f1..8b3fc6bbc51 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023-08-30 OpenCB +* Copyright 2015-2023-08-31 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java index b619c612c32..471a564c487 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023-08-30 OpenCB +* Copyright 2015-2023-08-31 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java index 408f28841f3..78ed32b92dc 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/OperationsVariantStorageCommandExecutor.java @@ -197,7 +197,7 @@ private RestResponse configureCellbase() throws Exception { putNestedIfNotEmpty(beanParams, "url",commandOptions.url, true); putNestedIfNotEmpty(beanParams, "version",commandOptions.version, true); putNestedIfNotEmpty(beanParams, "dataRelease",commandOptions.dataRelease, true); - putNestedIfNotEmpty(beanParams, "token",commandOptions.token, true); + putNestedIfNotEmpty(beanParams, "apiKey",commandOptions.apiKey, true); cellBaseConfiguration = JacksonUtils.getDefaultObjectMapper().copy() .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java index 7facd50d4d6..2ed3593e612 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/ProjectsCommandExecutor.java @@ -123,7 +123,7 @@ private RestResponse create() throws Exception { putNestedIfNotEmpty(beanParams, "cellbase.url",commandOptions.cellbaseUrl, true); putNestedIfNotEmpty(beanParams, "cellbase.version",commandOptions.cellbaseVersion, true); putNestedIfNotEmpty(beanParams, "cellbase.dataRelease",commandOptions.cellbaseDataRelease, true); - putNestedIfNotEmpty(beanParams, "cellbase.token",commandOptions.cellbaseToken, true); + putNestedIfNotEmpty(beanParams, "cellbase.apiKey",commandOptions.cellbaseApiKey, true); putNestedIfNotNull(beanParams, "attributes",commandOptions.attributes, true); projectCreateParams = JacksonUtils.getDefaultObjectMapper().copy() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/OperationsVariantStorageCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/OperationsVariantStorageCommandOptions.java index c3c89bf4b1a..d0b8a26d019 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/OperationsVariantStorageCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/OperationsVariantStorageCommandOptions.java @@ -128,8 +128,8 @@ public class ConfigureCellbaseCommandOptions { @Parameter(names = {"--data-release"}, description = "CellBase data release version to be used. If empty, will use the active one", required = false, arity = 1) public String dataRelease; - @Parameter(names = {"--token"}, description = "CellBase token to access to the licensed/restricted data sources such as COSMIC, HGMD,...", required = false, arity = 1) - public String token; + @Parameter(names = {"--api-key"}, description = "API key to access to the licensed/restricted data sources (COSMIC, HGMD,...) and to manage quota.", required = false, arity = 1) + public String apiKey; } diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/ProjectsCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/ProjectsCommandOptions.java index 1f7a3782e45..a2eca8cb958 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/ProjectsCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/ProjectsCommandOptions.java @@ -110,8 +110,8 @@ public class CreateCommandOptions { @Parameter(names = {"--cellbase-data-release"}, description = "CellBase data release version to be used. If empty, will use the active one", required = false, arity = 1) public String cellbaseDataRelease; - @Parameter(names = {"--cellbase-token"}, description = "CellBase token to access to the licensed/restricted data sources such as COSMIC, HGMD,...", required = false, arity = 1) - public String cellbaseToken; + @Parameter(names = {"--cellbase-api-key"}, description = "API key to access to the licensed/restricted data sources (COSMIC, HGMD,...) and to manage quota.", required = false, arity = 1) + public String cellbaseApiKey; @DynamicParameter(names = {"--attributes"}, description = "The body web service attributes parameter. Use: --attributes key=value", required = false) public java.util.Map attributes = new HashMap<>(); //Dynamic parameters must be initialized; diff --git a/opencga-client/src/main/R/R/Admin-methods.R b/opencga-client/src/main/R/R/Admin-methods.R index 5d46536451d..683aadd80e1 100644 --- a/opencga-client/src/main/R/R/Admin-methods.R +++ b/opencga-client/src/main/R/R/Admin-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-08-31 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Alignment-methods.R b/opencga-client/src/main/R/R/Alignment-methods.R index 206b0aa2646..175943692f6 100644 --- a/opencga-client/src/main/R/R/Alignment-methods.R +++ b/opencga-client/src/main/R/R/Alignment-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-08-31 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/AllGenerics.R b/opencga-client/src/main/R/R/AllGenerics.R index 8e9baedd284..088e6976532 100644 --- a/opencga-client/src/main/R/R/AllGenerics.R +++ b/opencga-client/src/main/R/R/AllGenerics.R @@ -1,31 +1,31 @@ # ############################################################################## ## UserClient -setGeneric("userClient", function(OpencgaR, user, filterId, users, endpointName, params=NULL, ...) +setGeneric("userClient", function(OpencgaR, filterId, users, user, endpointName, params=NULL, ...) standardGeneric("userClient")) # ############################################################################## ## ProjectClient -setGeneric("projectClient", function(OpencgaR, projects, project, endpointName, params=NULL, ...) +setGeneric("projectClient", function(OpencgaR, project, projects, endpointName, params=NULL, ...) standardGeneric("projectClient")) # ############################################################################## ## StudyClient -setGeneric("studyClient", function(OpencgaR, members, variableSet, studies, group, study, templateId, endpointName, params=NULL, ...) +setGeneric("studyClient", function(OpencgaR, members, variableSet, studies, study, templateId, group, endpointName, params=NULL, ...) standardGeneric("studyClient")) # ############################################################################## ## FileClient -setGeneric("fileClient", function(OpencgaR, files, members, file, annotationSet, folder, endpointName, params=NULL, ...) +setGeneric("fileClient", function(OpencgaR, members, annotationSet, file, files, folder, endpointName, params=NULL, ...) standardGeneric("fileClient")) # ############################################################################## ## JobClient -setGeneric("jobClient", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...) +setGeneric("jobClient", function(OpencgaR, job, members, jobs, endpointName, params=NULL, ...) standardGeneric("jobClient")) # ############################################################################## ## SampleClient -setGeneric("sampleClient", function(OpencgaR, members, sample, samples, annotationSet, endpointName, params=NULL, ...) +setGeneric("sampleClient", function(OpencgaR, samples, members, sample, annotationSet, endpointName, params=NULL, ...) standardGeneric("sampleClient")) # ############################################################################## @@ -35,12 +35,12 @@ setGeneric("individualClient", function(OpencgaR, members, individuals, annotati # ############################################################################## ## FamilyClient -setGeneric("familyClient", function(OpencgaR, members, family, annotationSet, families, endpointName, params=NULL, ...) +setGeneric("familyClient", function(OpencgaR, family, members, families, annotationSet, endpointName, params=NULL, ...) standardGeneric("familyClient")) # ############################################################################## ## CohortClient -setGeneric("cohortClient", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) +setGeneric("cohortClient", function(OpencgaR, members, cohort, annotationSet, cohorts, endpointName, params=NULL, ...) standardGeneric("cohortClient")) # ############################################################################## @@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## ClinicalClient -setGeneric("clinicalClient", function(OpencgaR, interpretations, members, interpretation, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...) +setGeneric("clinicalClient", function(OpencgaR, interpretation, members, interpretations, clinicalAnalyses, clinicalAnalysis, endpointName, params=NULL, ...) standardGeneric("clinicalClient")) # ############################################################################## @@ -75,7 +75,7 @@ setGeneric("metaClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## GA4GHClient -setGeneric("ga4ghClient", function(OpencgaR, file, study, endpointName, params=NULL, ...) +setGeneric("ga4ghClient", function(OpencgaR, study, file, endpointName, params=NULL, ...) standardGeneric("ga4ghClient")) # ############################################################################## diff --git a/opencga-client/src/main/R/R/Clinical-methods.R b/opencga-client/src/main/R/R/Clinical-methods.R index f0652ba64dd..b87af69bca9 100644 --- a/opencga-client/src/main/R/R/Clinical-methods.R +++ b/opencga-client/src/main/R/R/Clinical-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-08-31 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -58,7 +58,7 @@ #' [*]: Required parameter #' @export -setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, members, interpretation, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...) { +setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretation, members, interpretations, clinicalAnalyses, clinicalAnalysis, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R index 2bcb87bbbbc..4aafeeb7609 100644 --- a/opencga-client/src/main/R/R/Cohort-methods.R +++ b/opencga-client/src/main/R/R/Cohort-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-08-31 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("cohortClient", "OpencgaR", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) { +setMethod("cohortClient", "OpencgaR", function(OpencgaR, members, cohort, annotationSet, cohorts, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Family-methods.R b/opencga-client/src/main/R/R/Family-methods.R index 5993bbe8de9..069bac92a64 100644 --- a/opencga-client/src/main/R/R/Family-methods.R +++ b/opencga-client/src/main/R/R/Family-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-08-31 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("familyClient", "OpencgaR", function(OpencgaR, members, family, annotationSet, families, endpointName, params=NULL, ...) { +setMethod("familyClient", "OpencgaR", function(OpencgaR, family, members, families, annotationSet, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/families/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/File-methods.R b/opencga-client/src/main/R/R/File-methods.R index 0ef0d2c83d8..1db2de2c791 100644 --- a/opencga-client/src/main/R/R/File-methods.R +++ b/opencga-client/src/main/R/R/File-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-08-31 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -54,7 +54,7 @@ #' [*]: Required parameter #' @export -setMethod("fileClient", "OpencgaR", function(OpencgaR, files, members, file, annotationSet, folder, endpointName, params=NULL, ...) { +setMethod("fileClient", "OpencgaR", function(OpencgaR, members, annotationSet, file, files, folder, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/files/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/GA4GH-methods.R b/opencga-client/src/main/R/R/GA4GH-methods.R index 534e75260ad..3d4b5de60c2 100644 --- a/opencga-client/src/main/R/R/GA4GH-methods.R +++ b/opencga-client/src/main/R/R/GA4GH-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-08-31 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -31,7 +31,7 @@ #' [*]: Required parameter #' @export -setMethod("ga4ghClient", "OpencgaR", function(OpencgaR, file, study, endpointName, params=NULL, ...) { +setMethod("ga4ghClient", "OpencgaR", function(OpencgaR, study, file, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/ga4gh/reads/search: diff --git a/opencga-client/src/main/R/R/Individual-methods.R b/opencga-client/src/main/R/R/Individual-methods.R index 019acd410c2..348b34679a1 100644 --- a/opencga-client/src/main/R/R/Individual-methods.R +++ b/opencga-client/src/main/R/R/Individual-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-08-31 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Job-methods.R b/opencga-client/src/main/R/R/Job-methods.R index f85fe4840f7..59955bac486 100644 --- a/opencga-client/src/main/R/R/Job-methods.R +++ b/opencga-client/src/main/R/R/Job-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-08-31 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -40,7 +40,7 @@ #' [*]: Required parameter #' @export -setMethod("jobClient", "OpencgaR", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...) { +setMethod("jobClient", "OpencgaR", function(OpencgaR, job, members, jobs, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/jobs/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Meta-methods.R b/opencga-client/src/main/R/R/Meta-methods.R index d4de1c866b8..386dc6d24da 100644 --- a/opencga-client/src/main/R/R/Meta-methods.R +++ b/opencga-client/src/main/R/R/Meta-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-08-31 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Operation-methods.R b/opencga-client/src/main/R/R/Operation-methods.R index 902a0403f47..f143297e89e 100644 --- a/opencga-client/src/main/R/R/Operation-methods.R +++ b/opencga-client/src/main/R/R/Operation-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-08-31 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Panel-methods.R b/opencga-client/src/main/R/R/Panel-methods.R index e7d661d3a2c..1a7bf7bdbca 100644 --- a/opencga-client/src/main/R/R/Panel-methods.R +++ b/opencga-client/src/main/R/R/Panel-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-08-31 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Project-methods.R b/opencga-client/src/main/R/R/Project-methods.R index b4ab8a5b98e..3e68f49bfe5 100644 --- a/opencga-client/src/main/R/R/Project-methods.R +++ b/opencga-client/src/main/R/R/Project-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-08-31 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -34,7 +34,7 @@ #' [*]: Required parameter #' @export -setMethod("projectClient", "OpencgaR", function(OpencgaR, projects, project, endpointName, params=NULL, ...) { +setMethod("projectClient", "OpencgaR", function(OpencgaR, project, projects, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/projects/create: diff --git a/opencga-client/src/main/R/R/Sample-methods.R b/opencga-client/src/main/R/R/Sample-methods.R index 89b2d7b5876..a78d57987f3 100644 --- a/opencga-client/src/main/R/R/Sample-methods.R +++ b/opencga-client/src/main/R/R/Sample-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-08-31 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("sampleClient", "OpencgaR", function(OpencgaR, members, sample, samples, annotationSet, endpointName, params=NULL, ...) { +setMethod("sampleClient", "OpencgaR", function(OpencgaR, samples, members, sample, annotationSet, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/samples/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Study-methods.R b/opencga-client/src/main/R/R/Study-methods.R index 754fa677dea..682812a7583 100644 --- a/opencga-client/src/main/R/R/Study-methods.R +++ b/opencga-client/src/main/R/R/Study-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-08-31 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -46,7 +46,7 @@ #' [*]: Required parameter #' @export -setMethod("studyClient", "OpencgaR", function(OpencgaR, members, variableSet, studies, group, study, templateId, endpointName, params=NULL, ...) { +setMethod("studyClient", "OpencgaR", function(OpencgaR, members, variableSet, studies, study, templateId, group, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/studies/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/User-methods.R b/opencga-client/src/main/R/R/User-methods.R index 7fb54a32ff1..71089917286 100644 --- a/opencga-client/src/main/R/R/User-methods.R +++ b/opencga-client/src/main/R/R/User-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-08-31 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("userClient", "OpencgaR", function(OpencgaR, user, filterId, users, endpointName, params=NULL, ...) { +setMethod("userClient", "OpencgaR", function(OpencgaR, filterId, users, user, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/users/login: diff --git a/opencga-client/src/main/R/R/Variant-methods.R b/opencga-client/src/main/R/R/Variant-methods.R index 0b7a706cb8f..1925f53cf1d 100644 --- a/opencga-client/src/main/R/R/Variant-methods.R +++ b/opencga-client/src/main/R/R/Variant-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-08-31 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java index 2a375bb7b83..71bae1378cd 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java index 08257cc1a1a..e902d0d6454 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java @@ -40,7 +40,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java index 32ab712003e..012238a332a 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java @@ -51,7 +51,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java index 547601b9329..024ddc75a4c 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java @@ -37,7 +37,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java index ad5ea1a7047..ba7055998a1 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java @@ -35,7 +35,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java index d113cbdaf09..9b7142415e4 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java index 72be6ed305b..c40f63da5d7 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java @@ -43,7 +43,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java index fbb84f972a4..a4afee831af 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java @@ -27,7 +27,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java index 5803d125e54..2b291285857 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java index 27245d4011c..35e20d6ea8d 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java @@ -37,7 +37,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java index c2c015b670d..2a4c2afb9b8 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java @@ -28,7 +28,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java index 47aeec33622..b1dd2d4757b 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java @@ -32,7 +32,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java index d2dd71bc2f3..31b281cccd2 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java index 53502e91c7e..6e4fb4a9495 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java @@ -45,7 +45,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java index eda89cb9228..3443565c6a3 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java index 0d25391978a..fe1f4de3e99 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java @@ -62,7 +62,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java index ae6bef9d18d..e2b9052903e 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java @@ -50,7 +50,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Admin.js b/opencga-client/src/main/javascript/Admin.js index 26d6d454012..60a9d5b1c9e 100644 --- a/opencga-client/src/main/javascript/Admin.js +++ b/opencga-client/src/main/javascript/Admin.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Alignment.js b/opencga-client/src/main/javascript/Alignment.js index 33aa92db017..10a7da5bad2 100644 --- a/opencga-client/src/main/javascript/Alignment.js +++ b/opencga-client/src/main/javascript/Alignment.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/ClinicalAnalysis.js b/opencga-client/src/main/javascript/ClinicalAnalysis.js index 4434d811346..687447b8005 100644 --- a/opencga-client/src/main/javascript/ClinicalAnalysis.js +++ b/opencga-client/src/main/javascript/ClinicalAnalysis.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Cohort.js b/opencga-client/src/main/javascript/Cohort.js index cb53c5278a3..f121ff941f5 100644 --- a/opencga-client/src/main/javascript/Cohort.js +++ b/opencga-client/src/main/javascript/Cohort.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/DiseasePanel.js b/opencga-client/src/main/javascript/DiseasePanel.js index a4bc253c0bd..1216496f705 100644 --- a/opencga-client/src/main/javascript/DiseasePanel.js +++ b/opencga-client/src/main/javascript/DiseasePanel.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Family.js b/opencga-client/src/main/javascript/Family.js index e971b3b2e81..ea150256018 100644 --- a/opencga-client/src/main/javascript/Family.js +++ b/opencga-client/src/main/javascript/Family.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/File.js b/opencga-client/src/main/javascript/File.js index b3219c4f08a..80d2eac1817 100644 --- a/opencga-client/src/main/javascript/File.js +++ b/opencga-client/src/main/javascript/File.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/GA4GH.js b/opencga-client/src/main/javascript/GA4GH.js index ec01beb21de..41810680d69 100644 --- a/opencga-client/src/main/javascript/GA4GH.js +++ b/opencga-client/src/main/javascript/GA4GH.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Individual.js b/opencga-client/src/main/javascript/Individual.js index 71eb45dbafd..c611dbc3d20 100644 --- a/opencga-client/src/main/javascript/Individual.js +++ b/opencga-client/src/main/javascript/Individual.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Job.js b/opencga-client/src/main/javascript/Job.js index 1e1cc91bc52..e751db7fb46 100644 --- a/opencga-client/src/main/javascript/Job.js +++ b/opencga-client/src/main/javascript/Job.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Meta.js b/opencga-client/src/main/javascript/Meta.js index 24dfe87c63d..f49c2c01b37 100644 --- a/opencga-client/src/main/javascript/Meta.js +++ b/opencga-client/src/main/javascript/Meta.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Project.js b/opencga-client/src/main/javascript/Project.js index e240c25cb46..0e5880626c3 100644 --- a/opencga-client/src/main/javascript/Project.js +++ b/opencga-client/src/main/javascript/Project.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Sample.js b/opencga-client/src/main/javascript/Sample.js index 03c6a5b8d8f..21a7247620e 100644 --- a/opencga-client/src/main/javascript/Sample.js +++ b/opencga-client/src/main/javascript/Sample.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Study.js b/opencga-client/src/main/javascript/Study.js index e99e8c7606b..c9e4deb0aac 100644 --- a/opencga-client/src/main/javascript/Study.js +++ b/opencga-client/src/main/javascript/Study.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/User.js b/opencga-client/src/main/javascript/User.js index bfed2a7bfec..904b617010a 100644 --- a/opencga-client/src/main/javascript/User.js +++ b/opencga-client/src/main/javascript/User.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Variant.js b/opencga-client/src/main/javascript/Variant.js index ae9365d5448..3430052c798 100644 --- a/opencga-client/src/main/javascript/Variant.js +++ b/opencga-client/src/main/javascript/Variant.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/VariantOperation.js b/opencga-client/src/main/javascript/VariantOperation.js index f9837f69e25..5582f9cfd53 100644 --- a/opencga-client/src/main/javascript/VariantOperation.js +++ b/opencga-client/src/main/javascript/VariantOperation.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-08-31 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py index e982694d126..98954f3e971 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-08-31 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py index b94f350449a..7a9da2b0a02 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-08-31 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py index ca4e1438978..7c5b60dc1a3 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-08-31 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py index fef4cafa48d..0a3b30eab24 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-08-31 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py index 8382900c307..e5176a346f7 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-08-31 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py index 0637f728a08..198bccd8143 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-08-31 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py index 816cdf83c0b..8ef5f6a3cee 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-08-31 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py index 6f62ec62786..4ed3b96720b 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-08-31 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py index 3982f010208..34ec70ec784 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-08-31 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py index 313cf0df796..d12fbfa375a 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-08-31 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py index 189a5ab62ea..c334170020b 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-08-31 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py index 0784b20594c..f9c91a6177f 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-08-31 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py index 258189685ef..d9afbca66d7 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-08-31 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py index 3726c1e0a3a..5698145ea79 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-08-31 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py index 80ac433566b..36018f0560f 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-08-31 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py index 32dfa804648..c6143f58c4d 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-08-31 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py index 4070484d219..10e74c335a6 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-08-31 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. From 48889d0218db3d0c3779fa15ee956e4d72d2e350 Mon Sep 17 00:00:00 2001 From: pfurio Date: Fri, 1 Sep 2023 10:43:15 +0200 Subject: [PATCH 095/109] app: generate cli automatically, #TASK-4248 --- .../app/cli/main/OpenCgaCompleter.java | 2 +- .../app/cli/main/OpencgaCliOptionsParser.java | 2 +- .../AnalysisClinicalCommandOptions.java | 16 ++-- .../main/options/CohortsCommandOptions.java | 10 +-- .../options/DiseasePanelsCommandOptions.java | 32 ++++---- .../main/options/FamiliesCommandOptions.java | 16 ++-- .../cli/main/options/FilesCommandOptions.java | 20 ++--- .../options/IndividualsCommandOptions.java | 28 +++---- .../cli/main/options/JobsCommandOptions.java | 8 +- .../main/options/SamplesCommandOptions.java | 8 +- opencga-client/src/main/R/R/Admin-methods.R | 2 +- .../src/main/R/R/Alignment-methods.R | 2 +- opencga-client/src/main/R/R/AllGenerics.R | 20 ++--- .../src/main/R/R/Clinical-methods.R | 20 ++--- opencga-client/src/main/R/R/Cohort-methods.R | 14 ++-- opencga-client/src/main/R/R/Family-methods.R | 20 ++--- opencga-client/src/main/R/R/File-methods.R | 24 +++--- opencga-client/src/main/R/R/GA4GH-methods.R | 4 +- .../src/main/R/R/Individual-methods.R | 32 ++++---- opencga-client/src/main/R/R/Job-methods.R | 14 ++-- opencga-client/src/main/R/R/Meta-methods.R | 2 +- .../src/main/R/R/Operation-methods.R | 2 +- opencga-client/src/main/R/R/Panel-methods.R | 34 ++++----- opencga-client/src/main/R/R/Project-methods.R | 2 +- opencga-client/src/main/R/R/Sample-methods.R | 12 +-- opencga-client/src/main/R/R/Study-methods.R | 4 +- opencga-client/src/main/R/R/User-methods.R | 4 +- opencga-client/src/main/R/R/Variant-methods.R | 2 +- .../client/rest/clients/AdminClient.java | 2 +- .../client/rest/clients/AlignmentClient.java | 2 +- .../rest/clients/ClinicalAnalysisClient.java | 26 ++++--- .../client/rest/clients/CohortClient.java | 17 +++-- .../rest/clients/DiseasePanelClient.java | 54 ++++++++----- .../client/rest/clients/FamilyClient.java | 26 ++++--- .../client/rest/clients/FileClient.java | 32 +++++--- .../client/rest/clients/GA4GHClient.java | 2 +- .../client/rest/clients/IndividualClient.java | 44 +++++++---- .../client/rest/clients/JobClient.java | 17 +++-- .../client/rest/clients/MetaClient.java | 2 +- .../client/rest/clients/ProjectClient.java | 2 +- .../client/rest/clients/SampleClient.java | 14 ++-- .../client/rest/clients/StudyClient.java | 2 +- .../client/rest/clients/UserClient.java | 2 +- .../client/rest/clients/VariantClient.java | 2 +- .../rest/clients/VariantOperationClient.java | 2 +- opencga-client/src/main/javascript/Admin.js | 2 +- .../src/main/javascript/Alignment.js | 2 +- .../src/main/javascript/ClinicalAnalysis.js | 26 ++++--- opencga-client/src/main/javascript/Cohort.js | 17 +++-- .../src/main/javascript/DiseasePanel.js | 54 ++++++++----- opencga-client/src/main/javascript/Family.js | 26 ++++--- opencga-client/src/main/javascript/File.js | 32 +++++--- opencga-client/src/main/javascript/GA4GH.js | 2 +- .../src/main/javascript/Individual.js | 44 +++++++---- opencga-client/src/main/javascript/Job.js | 17 +++-- opencga-client/src/main/javascript/Meta.js | 2 +- opencga-client/src/main/javascript/Project.js | 2 +- opencga-client/src/main/javascript/Sample.js | 14 ++-- opencga-client/src/main/javascript/Study.js | 2 +- opencga-client/src/main/javascript/User.js | 2 +- opencga-client/src/main/javascript/Variant.js | 2 +- .../src/main/javascript/VariantOperation.js | 2 +- .../pyopencga/rest_clients/admin_client.py | 2 +- .../rest_clients/alignment_client.py | 2 +- .../rest_clients/clinical_analysis_client.py | 38 +++++++--- .../pyopencga/rest_clients/cohort_client.py | 21 +++-- .../rest_clients/disease_panel_client.py | 76 +++++++++++++++---- .../pyopencga/rest_clients/family_client.py | 28 ++++++- .../pyopencga/rest_clients/file_client.py | 48 +++++++++--- .../pyopencga/rest_clients/ga4gh_client.py | 2 +- .../rest_clients/individual_client.py | 60 ++++++++++++--- .../pyopencga/rest_clients/job_client.py | 23 +++++- .../pyopencga/rest_clients/meta_client.py | 2 +- .../pyopencga/rest_clients/project_client.py | 2 +- .../pyopencga/rest_clients/sample_client.py | 14 +++- .../pyopencga/rest_clients/study_client.py | 2 +- .../pyopencga/rest_clients/user_client.py | 2 +- .../pyopencga/rest_clients/variant_client.py | 2 +- .../rest_clients/variant_operation_client.py | 2 +- .../opencga/core/api/ParamConstants.java | 14 ++-- 80 files changed, 765 insertions(+), 427 deletions(-) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java index 6627d4d82f1..07cb922d522 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023-08-30 OpenCB +* Copyright 2015-2023-09-01 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java index b619c612c32..4e3e7ed1c1f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023-08-30 OpenCB +* Copyright 2015-2023-09-01 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java index 48261ca8a3c..95636ad4c3f 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisClinicalCommandOptions.java @@ -275,7 +275,7 @@ public class DistinctCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list of Clinical Analysis IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list of Clinical Analysis UUIDs up to a maximum of 100", required = false, arity = 1) @@ -284,7 +284,7 @@ public class DistinctCommandOptions { @Parameter(names = {"--type"}, description = "Clinical Analysis type", required = false, arity = 1) public String type; - @Parameter(names = {"--disorder"}, description = "Clinical Analysis disorder", required = false, arity = 1) + @Parameter(names = {"--disorder"}, description = "Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String disorder; @Parameter(names = {"--files"}, description = "Clinical Analysis files", required = false, arity = 1) @@ -364,7 +364,7 @@ public class DistinctInterpretationCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list of Interpretation IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list of Interpretation UUIDs up to a maximum of 100", required = false, arity = 1) @@ -376,7 +376,7 @@ public class DistinctInterpretationCommandOptions { @Parameter(names = {"--analyst-id"}, description = "Analyst ID", required = false, arity = 1) public String analystId; - @Parameter(names = {"--method-name"}, description = "Interpretation method name", required = false, arity = 1) + @Parameter(names = {"--method-name"}, description = "Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String methodName; @Parameter(names = {"--panels"}, description = "Interpretation panels", required = false, arity = 1) @@ -432,7 +432,7 @@ public class SearchInterpretationCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list of Interpretation IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list of Interpretation UUIDs up to a maximum of 100", required = false, arity = 1) @@ -444,7 +444,7 @@ public class SearchInterpretationCommandOptions { @Parameter(names = {"--analyst-id"}, description = "Analyst ID", required = false, arity = 1) public String analystId; - @Parameter(names = {"--method-name"}, description = "Interpretation method name", required = false, arity = 1) + @Parameter(names = {"--method-name"}, description = "Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String methodName; @Parameter(names = {"--panels"}, description = "Interpretation panels", required = false, arity = 1) @@ -1488,7 +1488,7 @@ public class SearchCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list of Clinical Analysis IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list of Clinical Analysis UUIDs up to a maximum of 100", required = false, arity = 1) @@ -1497,7 +1497,7 @@ public class SearchCommandOptions { @Parameter(names = {"--type"}, description = "Clinical Analysis type", required = false, arity = 1) public String type; - @Parameter(names = {"--disorder"}, description = "Clinical Analysis disorder", required = false, arity = 1) + @Parameter(names = {"--disorder"}, description = "Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String disorder; @Parameter(names = {"--files"}, description = "Clinical Analysis files", required = false, arity = 1) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/CohortsCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/CohortsCommandOptions.java index 13373914df4..03f08e58c9e 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/CohortsCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/CohortsCommandOptions.java @@ -242,10 +242,10 @@ public class DistinctCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list of cohort IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; - @Parameter(names = {"--name", "-n"}, description = "Comma separated list of cohort names up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--name", "-n"}, description = "Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String name; @Parameter(names = {"--uuid"}, description = "Comma separated list of cohort IDs up to a maximum of 100", required = false, arity = 1) @@ -334,7 +334,7 @@ public class GenerateCommandOptions { @Parameter(names = {"--status"}, description = "Filter by status", required = false, arity = 1) public String status; - @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names", required = false, arity = 1) + @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String phenotypes; @Parameter(names = {"--annotation"}, description = "Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0", required = false, arity = 1) @@ -411,10 +411,10 @@ public class SearchCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list of cohort IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; - @Parameter(names = {"--name", "-n"}, description = "Comma separated list of cohort names up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--name", "-n"}, description = "Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String name; @Parameter(names = {"--uuid"}, description = "Comma separated list of cohort IDs up to a maximum of 100", required = false, arity = 1) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/DiseasePanelsCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/DiseasePanelsCommandOptions.java index c6e353a7dca..1f0f1cbb9bc 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/DiseasePanelsCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/DiseasePanelsCommandOptions.java @@ -157,37 +157,37 @@ public class DistinctCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list of panel IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list of panel UUIDs up to a maximum of 100", required = false, arity = 1) public String uuid; - @Parameter(names = {"--name", "-n"}, description = "Comma separated list of panel names up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--name", "-n"}, description = "Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String name; @Parameter(names = {"--internal-status"}, description = "Filter by internal status", required = false, arity = 1) public String internalStatus; - @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names", required = false, arity = 1) + @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String disorders; - @Parameter(names = {"--variants"}, description = "Comma separated list of variant ids", required = false, arity = 1) + @Parameter(names = {"--variants"}, description = "Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String variants; - @Parameter(names = {"--genes"}, description = "Comma separated list of gene ids", required = false, arity = 1) + @Parameter(names = {"--genes"}, description = "Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String genes; @Parameter(names = {"--source"}, description = "Comma separated list of source ids or names.", required = false, arity = 1) public String source; - @Parameter(names = {"--regions"}, description = "Comma separated list of regions", required = false, arity = 1) + @Parameter(names = {"--regions"}, description = "Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String regions; - @Parameter(names = {"--categories"}, description = "Comma separated list of category names", required = false, arity = 1) + @Parameter(names = {"--categories"}, description = "Comma separated list of category names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String categories; - @Parameter(names = {"--tags"}, description = "Panel tags", required = false, arity = 1) + @Parameter(names = {"--tags"}, description = "Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String tags; @Parameter(names = {"--deleted"}, description = "Boolean to retrieve deleted entries", required = false, help = true, arity = 0) @@ -275,37 +275,37 @@ public class SearchCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list of panel IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list of panel UUIDs up to a maximum of 100", required = false, arity = 1) public String uuid; - @Parameter(names = {"--name", "-n"}, description = "Comma separated list of panel names up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--name", "-n"}, description = "Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String name; @Parameter(names = {"--internal-status"}, description = "Filter by internal status", required = false, arity = 1) public String internalStatus; - @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names", required = false, arity = 1) + @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String disorders; - @Parameter(names = {"--variants"}, description = "Comma separated list of variant ids", required = false, arity = 1) + @Parameter(names = {"--variants"}, description = "Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String variants; - @Parameter(names = {"--genes"}, description = "Comma separated list of gene ids", required = false, arity = 1) + @Parameter(names = {"--genes"}, description = "Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String genes; @Parameter(names = {"--source"}, description = "Comma separated list of source ids or names.", required = false, arity = 1) public String source; - @Parameter(names = {"--regions"}, description = "Comma separated list of regions", required = false, arity = 1) + @Parameter(names = {"--regions"}, description = "Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String regions; - @Parameter(names = {"--categories"}, description = "Comma separated list of category names", required = false, arity = 1) + @Parameter(names = {"--categories"}, description = "Comma separated list of category names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String categories; - @Parameter(names = {"--tags"}, description = "Panel tags", required = false, arity = 1) + @Parameter(names = {"--tags"}, description = "Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String tags; @Parameter(names = {"--deleted"}, description = "Boolean to retrieve deleted entries", required = false, help = true, arity = 0) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FamiliesCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FamiliesCommandOptions.java index 9530f60074d..3c57ef335ba 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FamiliesCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FamiliesCommandOptions.java @@ -252,10 +252,10 @@ public class DistinctCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list family IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list family IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; - @Parameter(names = {"--name", "-n"}, description = "Comma separated list family names up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--name", "-n"}, description = "Comma separated list family names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String name; @Parameter(names = {"--uuid"}, description = "Comma separated list family UUIDs up to a maximum of 100", required = false, arity = 1) @@ -270,10 +270,10 @@ public class DistinctCommandOptions { @Parameter(names = {"--samples"}, description = "Comma separated list of member's samples", required = false, arity = 1) public String samples; - @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names", required = false, arity = 1) + @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String phenotypes; - @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names", required = false, arity = 1) + @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String disorders; @Parameter(names = {"--creation-date", "--cd"}, description = "Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805", required = false, arity = 1) @@ -335,10 +335,10 @@ public class SearchCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list family IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list family IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; - @Parameter(names = {"--name", "-n"}, description = "Comma separated list family names up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--name", "-n"}, description = "Comma separated list family names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String name; @Parameter(names = {"--uuid"}, description = "Comma separated list family UUIDs up to a maximum of 100", required = false, arity = 1) @@ -353,10 +353,10 @@ public class SearchCommandOptions { @Parameter(names = {"--samples"}, description = "Comma separated list of member's samples", required = false, arity = 1) public String samples; - @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names", required = false, arity = 1) + @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String phenotypes; - @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names", required = false, arity = 1) + @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String disorders; @Parameter(names = {"--creation-date", "--cd"}, description = "Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805", required = false, arity = 1) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FilesCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FilesCommandOptions.java index d1d4e0bf0a8..5ea18955f58 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FilesCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/FilesCommandOptions.java @@ -327,19 +327,19 @@ public class DistinctCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list of file IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of file IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list file UUIDs up to a maximum of 100", required = false, arity = 1) public String uuid; - @Parameter(names = {"--name", "-n"}, description = "Comma separated list of file names", required = false, arity = 1) + @Parameter(names = {"--name", "-n"}, description = "Comma separated list of file names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String name; - @Parameter(names = {"--path"}, description = "Comma separated list of paths", required = false, arity = 1) + @Parameter(names = {"--path"}, description = "Comma separated list of paths. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String path; - @Parameter(names = {"--uri", "--input", "-i"}, description = "Comma separated list of uris", required = false, arity = 1) + @Parameter(names = {"--uri", "--input", "-i"}, description = "Comma separated list of uris. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String uri; @Parameter(names = {"--type"}, description = "File type, either FILE or DIRECTORY", required = false, arity = 1) @@ -378,7 +378,7 @@ public class DistinctCommandOptions { @Parameter(names = {"--description"}, description = "Description", required = false, arity = 1) public String description; - @Parameter(names = {"--tags"}, description = "Tags", required = false, arity = 1) + @Parameter(names = {"--tags"}, description = "Tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String tags; @Parameter(names = {"--size"}, description = "File size", required = false, arity = 1) @@ -609,19 +609,19 @@ public class SearchCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list of file IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of file IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list file UUIDs up to a maximum of 100", required = false, arity = 1) public String uuid; - @Parameter(names = {"--name", "-n"}, description = "Comma separated list of file names", required = false, arity = 1) + @Parameter(names = {"--name", "-n"}, description = "Comma separated list of file names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String name; - @Parameter(names = {"--path"}, description = "Comma separated list of paths", required = false, arity = 1) + @Parameter(names = {"--path"}, description = "Comma separated list of paths. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String path; - @Parameter(names = {"--uri", "--input", "-i"}, description = "Comma separated list of uris", required = false, arity = 1) + @Parameter(names = {"--uri", "--input", "-i"}, description = "Comma separated list of uris. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String uri; @Parameter(names = {"--type"}, description = "File type, either FILE or DIRECTORY", required = false, arity = 1) @@ -660,7 +660,7 @@ public class SearchCommandOptions { @Parameter(names = {"--description"}, description = "Description", required = false, arity = 1) public String description; - @Parameter(names = {"--tags"}, description = "Tags", required = false, arity = 1) + @Parameter(names = {"--tags"}, description = "Tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String tags; @Parameter(names = {"--size"}, description = "File size", required = false, arity = 1) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/IndividualsCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/IndividualsCommandOptions.java index a9e20c70232..d0238597f52 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/IndividualsCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/IndividualsCommandOptions.java @@ -350,13 +350,13 @@ public class DistinctCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list individual IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list individual IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list individual UUIDs up to a maximum of 100", required = false, arity = 1) public String uuid; - @Parameter(names = {"--name", "-n"}, description = "Comma separated list individual names up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--name", "-n"}, description = "Comma separated list individual names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String name; @Parameter(names = {"--family-ids"}, description = "Comma separated list of family ids the individuals may belong to.", required = false, arity = 1) @@ -374,22 +374,22 @@ public class DistinctCommandOptions { @Parameter(names = {"--sex"}, description = "Individual sex", required = false, arity = 1) public String sex; - @Parameter(names = {"--ethnicity"}, description = "Individual ethnicity", required = false, arity = 1) + @Parameter(names = {"--ethnicity"}, description = "Individual ethnicity. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String ethnicity; @Parameter(names = {"--date-of-birth"}, description = "Individual date of birth", required = false, arity = 1) public String dateOfBirth; - @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names", required = false, arity = 1) + @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String disorders; - @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names", required = false, arity = 1) + @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String phenotypes; - @Parameter(names = {"--population-name"}, description = "Population name", required = false, arity = 1) + @Parameter(names = {"--population-name"}, description = "Population name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String populationName; - @Parameter(names = {"--population-subpopulation"}, description = "Subpopulation name", required = false, arity = 1) + @Parameter(names = {"--population-subpopulation"}, description = "Subpopulation name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String populationSubpopulation; @Parameter(names = {"--karyotypic-sex"}, description = "Individual karyotypic sex", required = false, arity = 1) @@ -457,13 +457,13 @@ public class SearchCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list individual IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list individual IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list individual UUIDs up to a maximum of 100", required = false, arity = 1) public String uuid; - @Parameter(names = {"--name", "-n"}, description = "Comma separated list individual names up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--name", "-n"}, description = "Comma separated list individual names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String name; @Parameter(names = {"--father"}, description = "Father ID, name or UUID", required = false, arity = 1) @@ -484,19 +484,19 @@ public class SearchCommandOptions { @Parameter(names = {"--date-of-birth"}, description = "Individual date of birth", required = false, arity = 1) public String dateOfBirth; - @Parameter(names = {"--ethnicity"}, description = "Individual ethnicity", required = false, arity = 1) + @Parameter(names = {"--ethnicity"}, description = "Individual ethnicity. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String ethnicity; - @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names", required = false, arity = 1) + @Parameter(names = {"--disorders"}, description = "Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String disorders; - @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names", required = false, arity = 1) + @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String phenotypes; - @Parameter(names = {"--population-name"}, description = "Population name", required = false, arity = 1) + @Parameter(names = {"--population-name"}, description = "Population name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String populationName; - @Parameter(names = {"--population-subpopulation"}, description = "Subpopulation name", required = false, arity = 1) + @Parameter(names = {"--population-subpopulation"}, description = "Subpopulation name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String populationSubpopulation; @Parameter(names = {"--karyotypic-sex"}, description = "Individual karyotypic sex", required = false, arity = 1) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/JobsCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/JobsCommandOptions.java index 44eac65bf28..04b6caae03c 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/JobsCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/JobsCommandOptions.java @@ -241,13 +241,13 @@ public class DistinctCommandOptions { @Parameter(names = {"--other-studies"}, description = "Flag indicating the entries being queried can belong to any related study, not just the primary one.", required = false, help = true, arity = 0) public boolean otherStudies = false; - @Parameter(names = {"--id"}, description = "Comma separated list of job IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of job IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list of job UUIDs up to a maximum of 100", required = false, arity = 1) public String uuid; - @Parameter(names = {"--tool-id"}, description = "Tool ID executed by the job", required = false, arity = 1) + @Parameter(names = {"--tool-id"}, description = "Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String toolId; @Parameter(names = {"--tool-type"}, description = "Tool type executed by the job [OPERATION, ANALYSIS]", required = false, arity = 1) @@ -362,13 +362,13 @@ public class SearchCommandOptions { @Parameter(names = {"--other-studies"}, description = "Flag indicating the entries being queried can belong to any related study, not just the primary one.", required = false, help = true, arity = 0) public boolean otherStudies = false; - @Parameter(names = {"--id"}, description = "Comma separated list of job IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list of job IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list of job UUIDs up to a maximum of 100", required = false, arity = 1) public String uuid; - @Parameter(names = {"--tool-id"}, description = "Tool ID executed by the job", required = false, arity = 1) + @Parameter(names = {"--tool-id"}, description = "Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String toolId; @Parameter(names = {"--tool-type"}, description = "Tool type executed by the job [OPERATION, ANALYSIS]", required = false, arity = 1) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/SamplesCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/SamplesCommandOptions.java index 0099fbf2a90..8cfc8fed346 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/SamplesCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/SamplesCommandOptions.java @@ -305,7 +305,7 @@ public class DistinctCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list sample IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list sample IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list sample UUIDs up to a maximum of 100", required = false, arity = 1) @@ -356,7 +356,7 @@ public class DistinctCommandOptions { @Parameter(names = {"--collection-method"}, description = "Collection method", required = false, arity = 1) public String collectionMethod; - @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names", required = false, arity = 1) + @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String phenotypes; @Parameter(names = {"--annotation"}, description = "Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0", required = false, arity = 1) @@ -468,7 +468,7 @@ public class SearchCommandOptions { @Parameter(names = {"--study", "-s"}, description = "Study [[user@]project:]study where study and project can be either the ID or UUID", required = false, arity = 1) public String study; - @Parameter(names = {"--id"}, description = "Comma separated list sample IDs up to a maximum of 100", required = false, arity = 1) + @Parameter(names = {"--id"}, description = "Comma separated list sample IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String id; @Parameter(names = {"--uuid"}, description = "Comma separated list sample UUIDs up to a maximum of 100", required = false, arity = 1) @@ -519,7 +519,7 @@ public class SearchCommandOptions { @Parameter(names = {"--collection-method"}, description = "Collection method", required = false, arity = 1) public String collectionMethod; - @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names", required = false, arity = 1) + @Parameter(names = {"--phenotypes"}, description = "Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.", required = false, arity = 1) public String phenotypes; @Parameter(names = {"--annotation"}, description = "Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0", required = false, arity = 1) diff --git a/opencga-client/src/main/R/R/Admin-methods.R b/opencga-client/src/main/R/R/Admin-methods.R index 5d46536451d..da576e61ed5 100644 --- a/opencga-client/src/main/R/R/Admin-methods.R +++ b/opencga-client/src/main/R/R/Admin-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Alignment-methods.R b/opencga-client/src/main/R/R/Alignment-methods.R index 206b0aa2646..e8d0ded651f 100644 --- a/opencga-client/src/main/R/R/Alignment-methods.R +++ b/opencga-client/src/main/R/R/Alignment-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/AllGenerics.R b/opencga-client/src/main/R/R/AllGenerics.R index 8e9baedd284..64aa34c799c 100644 --- a/opencga-client/src/main/R/R/AllGenerics.R +++ b/opencga-client/src/main/R/R/AllGenerics.R @@ -1,6 +1,6 @@ # ############################################################################## ## UserClient -setGeneric("userClient", function(OpencgaR, user, filterId, users, endpointName, params=NULL, ...) +setGeneric("userClient", function(OpencgaR, filterId, users, user, endpointName, params=NULL, ...) standardGeneric("userClient")) # ############################################################################## @@ -10,37 +10,37 @@ setGeneric("projectClient", function(OpencgaR, projects, project, endpointName, # ############################################################################## ## StudyClient -setGeneric("studyClient", function(OpencgaR, members, variableSet, studies, group, study, templateId, endpointName, params=NULL, ...) +setGeneric("studyClient", function(OpencgaR, variableSet, studies, members, group, study, templateId, endpointName, params=NULL, ...) standardGeneric("studyClient")) # ############################################################################## ## FileClient -setGeneric("fileClient", function(OpencgaR, files, members, file, annotationSet, folder, endpointName, params=NULL, ...) +setGeneric("fileClient", function(OpencgaR, members, folder, annotationSet, files, file, endpointName, params=NULL, ...) standardGeneric("fileClient")) # ############################################################################## ## JobClient -setGeneric("jobClient", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...) +setGeneric("jobClient", function(OpencgaR, job, members, jobs, endpointName, params=NULL, ...) standardGeneric("jobClient")) # ############################################################################## ## SampleClient -setGeneric("sampleClient", function(OpencgaR, members, sample, samples, annotationSet, endpointName, params=NULL, ...) +setGeneric("sampleClient", function(OpencgaR, annotationSet, sample, samples, members, endpointName, params=NULL, ...) standardGeneric("sampleClient")) # ############################################################################## ## IndividualClient -setGeneric("individualClient", function(OpencgaR, members, individuals, annotationSet, individual, endpointName, params=NULL, ...) +setGeneric("individualClient", function(OpencgaR, individual, individuals, annotationSet, members, endpointName, params=NULL, ...) standardGeneric("individualClient")) # ############################################################################## ## FamilyClient -setGeneric("familyClient", function(OpencgaR, members, family, annotationSet, families, endpointName, params=NULL, ...) +setGeneric("familyClient", function(OpencgaR, families, family, annotationSet, members, endpointName, params=NULL, ...) standardGeneric("familyClient")) # ############################################################################## ## CohortClient -setGeneric("cohortClient", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) +setGeneric("cohortClient", function(OpencgaR, annotationSet, cohorts, members, cohort, endpointName, params=NULL, ...) standardGeneric("cohortClient")) # ############################################################################## @@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## ClinicalClient -setGeneric("clinicalClient", function(OpencgaR, interpretations, members, interpretation, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...) +setGeneric("clinicalClient", function(OpencgaR, interpretation, members, interpretations, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...) standardGeneric("clinicalClient")) # ############################################################################## @@ -75,7 +75,7 @@ setGeneric("metaClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## GA4GHClient -setGeneric("ga4ghClient", function(OpencgaR, file, study, endpointName, params=NULL, ...) +setGeneric("ga4ghClient", function(OpencgaR, study, file, endpointName, params=NULL, ...) standardGeneric("ga4ghClient")) # ############################################################################## diff --git a/opencga-client/src/main/R/R/Clinical-methods.R b/opencga-client/src/main/R/R/Clinical-methods.R index f0652ba64dd..ae64c192aeb 100644 --- a/opencga-client/src/main/R/R/Clinical-methods.R +++ b/opencga-client/src/main/R/R/Clinical-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -58,7 +58,7 @@ #' [*]: Required parameter #' @export -setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, members, interpretation, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...) { +setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretation, members, interpretations, clinicalAnalysis, clinicalAnalyses, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update: @@ -94,10 +94,10 @@ setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, memb #' @section Endpoint /{apiVersion}/analysis/clinical/distinct: #' Clinical Analysis distinct method. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list of Clinical Analysis IDs up to a maximum of 100. + #' @param id Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. #' @param type Clinical Analysis type. - #' @param disorder Clinical Analysis disorder. + #' @param disorder Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param files Clinical Analysis files. #' @param sample Sample associated to the proband or any member of a family. #' @param individual Proband or any member of a family. @@ -126,11 +126,11 @@ setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, memb #' @section Endpoint /{apiVersion}/analysis/clinical/interpretation/distinct: #' Interpretation distinct method. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list of Interpretation IDs up to a maximum of 100. + #' @param id Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list of Interpretation UUIDs up to a maximum of 100. #' @param clinicalAnalysisId Clinical Analysis id. #' @param analystId Analyst ID. - #' @param methodName Interpretation method name. + #' @param methodName Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param panels Interpretation panels. #' @param primaryFindings Interpretation primary findings. #' @param secondaryFindings Interpretation secondary findings. @@ -152,11 +152,11 @@ setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, memb #' @param skip Number of results to skip. #' @param sort Sort the results. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list of Interpretation IDs up to a maximum of 100. + #' @param id Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list of Interpretation UUIDs up to a maximum of 100. #' @param clinicalAnalysisId Clinical Analysis id. #' @param analystId Analyst ID. - #' @param methodName Interpretation method name. + #' @param methodName Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param panels Interpretation panels. #' @param primaryFindings Interpretation primary findings. #' @param secondaryFindings Interpretation secondary findings. @@ -484,10 +484,10 @@ setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretations, memb #' @param skip Number of results to skip. #' @param count Get the total number of results matching the query. Deactivated by default. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list of Clinical Analysis IDs up to a maximum of 100. + #' @param id Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. #' @param type Clinical Analysis type. - #' @param disorder Clinical Analysis disorder. + #' @param disorder Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param files Clinical Analysis files. #' @param sample Sample associated to the proband or any member of a family. #' @param individual Proband or any member of a family. diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R index 2bcb87bbbbc..3dbf84870e5 100644 --- a/opencga-client/src/main/R/R/Cohort-methods.R +++ b/opencga-client/src/main/R/R/Cohort-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("cohortClient", "OpencgaR", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) { +setMethod("cohortClient", "OpencgaR", function(OpencgaR, annotationSet, cohorts, members, cohort, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update: @@ -97,8 +97,8 @@ setMethod("cohortClient", "OpencgaR", function(OpencgaR, members, annotationSet, #' @section Endpoint /{apiVersion}/cohorts/distinct: #' Cohort distinct method. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list of cohort IDs up to a maximum of 100. - #' @param name Comma separated list of cohort names up to a maximum of 100. + #' @param id Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param name Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list of cohort IDs up to a maximum of 100. #' @param type Cohort type. #' @param creationDate creationDate. @@ -128,7 +128,7 @@ setMethod("cohortClient", "OpencgaR", function(OpencgaR, members, annotationSet, #' @param modificationDate Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. #' @param internalStatus Filter by internal status. #' @param status Filter by status. - #' @param phenotypes Comma separated list of phenotype ids or names. + #' @param phenotypes Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param annotation Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. #' @param acl Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example: acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which user john has both WRITE and WRITE_ANNOTATIONS permissions. Only study owners or administrators can query by this field. . #' @param release Release when it was created. @@ -147,8 +147,8 @@ setMethod("cohortClient", "OpencgaR", function(OpencgaR, members, annotationSet, #' @param count Get the total number of results matching the query. Deactivated by default. #' @param flattenAnnotations Flatten the annotations?. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list of cohort IDs up to a maximum of 100. - #' @param name Comma separated list of cohort names up to a maximum of 100. + #' @param id Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param name Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list of cohort IDs up to a maximum of 100. #' @param type Cohort type. #' @param creationDate creationDate. diff --git a/opencga-client/src/main/R/R/Family-methods.R b/opencga-client/src/main/R/R/Family-methods.R index 5993bbe8de9..c5d4cbc0485 100644 --- a/opencga-client/src/main/R/R/Family-methods.R +++ b/opencga-client/src/main/R/R/Family-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("familyClient", "OpencgaR", function(OpencgaR, members, family, annotationSet, families, endpointName, params=NULL, ...) { +setMethod("familyClient", "OpencgaR", function(OpencgaR, families, family, annotationSet, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/families/acl/{members}/update: @@ -98,14 +98,14 @@ setMethod("familyClient", "OpencgaR", function(OpencgaR, members, family, annota #' @section Endpoint /{apiVersion}/families/distinct: #' Family distinct method. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list family IDs up to a maximum of 100. - #' @param name Comma separated list family names up to a maximum of 100. + #' @param id Comma separated list family IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param name Comma separated list family names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list family UUIDs up to a maximum of 100. #' @param members Comma separated list of family members. #' @param expectedSize Expected size of the family (number of members). #' @param samples Comma separated list of member's samples. - #' @param phenotypes Comma separated list of phenotype ids or names. - #' @param disorders Comma separated list of disorder ids or names. + #' @param phenotypes Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param disorders Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param creationDate Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. #' @param modificationDate Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. #' @param deleted Boolean to retrieve deleted entries. @@ -128,14 +128,14 @@ setMethod("familyClient", "OpencgaR", function(OpencgaR, members, family, annota #' @param count Get the total number of results matching the query. Deactivated by default. #' @param flattenAnnotations Flatten the annotations?. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list family IDs up to a maximum of 100. - #' @param name Comma separated list family names up to a maximum of 100. + #' @param id Comma separated list family IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param name Comma separated list family names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list family UUIDs up to a maximum of 100. #' @param members Comma separated list of family members. #' @param expectedSize Expected size of the family (number of members). #' @param samples Comma separated list of member's samples. - #' @param phenotypes Comma separated list of phenotype ids or names. - #' @param disorders Comma separated list of disorder ids or names. + #' @param phenotypes Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param disorders Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param creationDate Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. #' @param modificationDate Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. #' @param deleted Boolean to retrieve deleted entries. diff --git a/opencga-client/src/main/R/R/File-methods.R b/opencga-client/src/main/R/R/File-methods.R index 0ef0d2c83d8..3145654d92d 100644 --- a/opencga-client/src/main/R/R/File-methods.R +++ b/opencga-client/src/main/R/R/File-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -54,7 +54,7 @@ #' [*]: Required parameter #' @export -setMethod("fileClient", "OpencgaR", function(OpencgaR, files, members, file, annotationSet, folder, endpointName, params=NULL, ...) { +setMethod("fileClient", "OpencgaR", function(OpencgaR, members, folder, annotationSet, files, file, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/files/acl/{members}/update: @@ -122,11 +122,11 @@ setMethod("fileClient", "OpencgaR", function(OpencgaR, files, members, file, ann #' @section Endpoint /{apiVersion}/files/distinct: #' File distinct method. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list of file IDs up to a maximum of 100. + #' @param id Comma separated list of file IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list file UUIDs up to a maximum of 100. - #' @param name Comma separated list of file names. - #' @param path Comma separated list of paths. - #' @param uri Comma separated list of uris. + #' @param name Comma separated list of file names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param path Comma separated list of paths. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param uri Comma separated list of uris. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param type File type, either FILE or DIRECTORY. #' @param bioformat Comma separated Bioformat values. For existing Bioformats see files/bioformats. #' @param format Comma separated Format values. For existing Formats see files/formats. @@ -139,7 +139,7 @@ setMethod("fileClient", "OpencgaR", function(OpencgaR, files, members, file, ann #' @param creationDate Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. #' @param modificationDate Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. #' @param description Description. - #' @param tags Tags. + #' @param tags Tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param size File size. #' @param sampleIds Comma separated list sample IDs or UUIDs up to a maximum of 100. #' @param jobId Job ID that created the file(s) or folder(s). @@ -207,11 +207,11 @@ setMethod("fileClient", "OpencgaR", function(OpencgaR, files, members, file, ann #' @param count Get the total number of results matching the query. Deactivated by default. #' @param flattenAnnotations Boolean indicating to flatten the annotations. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list of file IDs up to a maximum of 100. + #' @param id Comma separated list of file IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list file UUIDs up to a maximum of 100. - #' @param name Comma separated list of file names. - #' @param path Comma separated list of paths. - #' @param uri Comma separated list of uris. + #' @param name Comma separated list of file names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param path Comma separated list of paths. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param uri Comma separated list of uris. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param type File type, either FILE or DIRECTORY. #' @param bioformat Comma separated Bioformat values. For existing Bioformats see files/bioformats. #' @param format Comma separated Format values. For existing Formats see files/formats. @@ -224,7 +224,7 @@ setMethod("fileClient", "OpencgaR", function(OpencgaR, files, members, file, ann #' @param creationDate Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. #' @param modificationDate Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. #' @param description Description. - #' @param tags Tags. + #' @param tags Tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param size File size. #' @param sampleIds Comma separated list sample IDs or UUIDs up to a maximum of 100. #' @param jobId Job ID that created the file(s) or folder(s). diff --git a/opencga-client/src/main/R/R/GA4GH-methods.R b/opencga-client/src/main/R/R/GA4GH-methods.R index 534e75260ad..7ec25d1cb31 100644 --- a/opencga-client/src/main/R/R/GA4GH-methods.R +++ b/opencga-client/src/main/R/R/GA4GH-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -31,7 +31,7 @@ #' [*]: Required parameter #' @export -setMethod("ga4ghClient", "OpencgaR", function(OpencgaR, file, study, endpointName, params=NULL, ...) { +setMethod("ga4ghClient", "OpencgaR", function(OpencgaR, study, file, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/ga4gh/reads/search: diff --git a/opencga-client/src/main/R/R/Individual-methods.R b/opencga-client/src/main/R/R/Individual-methods.R index 019acd410c2..fa208ff5bf2 100644 --- a/opencga-client/src/main/R/R/Individual-methods.R +++ b/opencga-client/src/main/R/R/Individual-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("individualClient", "OpencgaR", function(OpencgaR, members, individuals, annotationSet, individual, endpointName, params=NULL, ...) { +setMethod("individualClient", "OpencgaR", function(OpencgaR, individual, individuals, annotationSet, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/individuals/acl/{members}/update: @@ -106,20 +106,20 @@ setMethod("individualClient", "OpencgaR", function(OpencgaR, members, individual #' @section Endpoint /{apiVersion}/individuals/distinct: #' Individual distinct method. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list individual IDs up to a maximum of 100. + #' @param id Comma separated list individual IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list individual UUIDs up to a maximum of 100. - #' @param name Comma separated list individual names up to a maximum of 100. + #' @param name Comma separated list individual names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param familyIds Comma separated list of family ids the individuals may belong to. #' @param father Father ID, name or UUID. #' @param mother Mother ID, name or UUID. #' @param samples Sample ID, name or UUID. #' @param sex Individual sex. - #' @param ethnicity Individual ethnicity. + #' @param ethnicity Individual ethnicity. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param dateOfBirth Individual date of birth. - #' @param disorders Comma separated list of disorder ids or names. - #' @param phenotypes Comma separated list of phenotype ids or names. - #' @param populationName Population name. - #' @param populationSubpopulation Subpopulation name. + #' @param disorders Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param phenotypes Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param populationName Population name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param populationSubpopulation Subpopulation name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param karyotypicSex Individual karyotypic sex. #' @param lifeStatus Individual life status. #' @param internalStatus Filter by internal status. @@ -144,20 +144,20 @@ setMethod("individualClient", "OpencgaR", function(OpencgaR, members, individual #' @param count Get the total number of results matching the query. Deactivated by default. #' @param flattenAnnotations Flatten the annotations?. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list individual IDs up to a maximum of 100. + #' @param id Comma separated list individual IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list individual UUIDs up to a maximum of 100. - #' @param name Comma separated list individual names up to a maximum of 100. + #' @param name Comma separated list individual names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param father Father ID, name or UUID. #' @param mother Mother ID, name or UUID. #' @param samples Sample ID, name or UUID. #' @param familyIds Comma separated list of family ids the individuals may belong to. #' @param sex Individual sex. #' @param dateOfBirth Individual date of birth. - #' @param ethnicity Individual ethnicity. - #' @param disorders Comma separated list of disorder ids or names. - #' @param phenotypes Comma separated list of phenotype ids or names. - #' @param populationName Population name. - #' @param populationSubpopulation Subpopulation name. + #' @param ethnicity Individual ethnicity. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param disorders Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param phenotypes Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param populationName Population name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param populationSubpopulation Subpopulation name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param karyotypicSex Individual karyotypic sex. #' @param lifeStatus Individual life status. #' @param internalStatus Filter by internal status. diff --git a/opencga-client/src/main/R/R/Job-methods.R b/opencga-client/src/main/R/R/Job-methods.R index f85fe4840f7..00c06ed1483 100644 --- a/opencga-client/src/main/R/R/Job-methods.R +++ b/opencga-client/src/main/R/R/Job-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -40,7 +40,7 @@ #' [*]: Required parameter #' @export -setMethod("jobClient", "OpencgaR", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...) { +setMethod("jobClient", "OpencgaR", function(OpencgaR, job, members, jobs, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/jobs/acl/{members}/update: @@ -87,9 +87,9 @@ setMethod("jobClient", "OpencgaR", function(OpencgaR, members, job, jobs, endpoi #' Job distinct method. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. #' @param otherStudies Flag indicating the entries being queried can belong to any related study, not just the primary one. - #' @param id Comma separated list of job IDs up to a maximum of 100. + #' @param id Comma separated list of job IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list of job UUIDs up to a maximum of 100. - #' @param toolId Tool ID executed by the job. + #' @param toolId Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param toolType Tool type executed by the job [OPERATION, ANALYSIS]. #' @param userId User that created the job. #' @param priority Priority of the job. @@ -128,9 +128,9 @@ setMethod("jobClient", "OpencgaR", function(OpencgaR, members, job, jobs, endpoi #' @param count Get the total number of results matching the query. Deactivated by default. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. #' @param otherStudies Flag indicating the entries being queried can belong to any related study, not just the primary one. - #' @param id Comma separated list of job IDs up to a maximum of 100. + #' @param id Comma separated list of job IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list of job UUIDs up to a maximum of 100. - #' @param toolId Tool ID executed by the job. + #' @param toolId Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param toolType Tool type executed by the job [OPERATION, ANALYSIS]. #' @param userId User that created the job. #' @param priority Priority of the job. @@ -155,7 +155,7 @@ setMethod("jobClient", "OpencgaR", function(OpencgaR, members, job, jobs, endpoi #' @param internalStatus Filter by internal status. #' @param priority Priority of the job. #' @param userId User that created the job. - #' @param toolId Tool ID executed by the job. + #' @param toolId Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. top=fetchOpenCGA(object=OpencgaR, category="jobs", categoryId=NULL, subcategory=NULL, subcategoryId=NULL, action="top", params=params, httpMethod="GET", as.queryParam=NULL, ...), diff --git a/opencga-client/src/main/R/R/Meta-methods.R b/opencga-client/src/main/R/R/Meta-methods.R index d4de1c866b8..360a9dacb50 100644 --- a/opencga-client/src/main/R/R/Meta-methods.R +++ b/opencga-client/src/main/R/R/Meta-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Operation-methods.R b/opencga-client/src/main/R/R/Operation-methods.R index 902a0403f47..f95d93bc801 100644 --- a/opencga-client/src/main/R/R/Operation-methods.R +++ b/opencga-client/src/main/R/R/Operation-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Panel-methods.R b/opencga-client/src/main/R/R/Panel-methods.R index e7d661d3a2c..fe01d294f0b 100644 --- a/opencga-client/src/main/R/R/Panel-methods.R +++ b/opencga-client/src/main/R/R/Panel-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -62,17 +62,17 @@ setMethod("panelClient", "OpencgaR", function(OpencgaR, members, panels, endpoin #' @section Endpoint /{apiVersion}/panels/distinct: #' Panel distinct method. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list of panel IDs up to a maximum of 100. + #' @param id Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list of panel UUIDs up to a maximum of 100. - #' @param name Comma separated list of panel names up to a maximum of 100. + #' @param name Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param internalStatus Filter by internal status. - #' @param disorders Comma separated list of disorder ids or names. - #' @param variants Comma separated list of variant ids. - #' @param genes Comma separated list of gene ids. + #' @param disorders Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param variants Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param genes Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param source Comma separated list of source ids or names. - #' @param regions Comma separated list of regions. - #' @param categories Comma separated list of category names. - #' @param tags Panel tags. + #' @param regions Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param categories Comma separated list of category names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param tags Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param deleted Boolean to retrieve deleted entries. #' @param status Filter by status. #' @param creationDate Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. @@ -103,17 +103,17 @@ setMethod("panelClient", "OpencgaR", function(OpencgaR, members, panels, endpoin #' @param skip Number of results to skip. #' @param count Get the total number of results matching the query. Deactivated by default. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list of panel IDs up to a maximum of 100. + #' @param id Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list of panel UUIDs up to a maximum of 100. - #' @param name Comma separated list of panel names up to a maximum of 100. + #' @param name Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param internalStatus Filter by internal status. - #' @param disorders Comma separated list of disorder ids or names. - #' @param variants Comma separated list of variant ids. - #' @param genes Comma separated list of gene ids. + #' @param disorders Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param variants Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param genes Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param source Comma separated list of source ids or names. - #' @param regions Comma separated list of regions. - #' @param categories Comma separated list of category names. - #' @param tags Panel tags. + #' @param regions Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param categories Comma separated list of category names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + #' @param tags Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param deleted Boolean to retrieve deleted entries. #' @param status Filter by status. #' @param creationDate Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. diff --git a/opencga-client/src/main/R/R/Project-methods.R b/opencga-client/src/main/R/R/Project-methods.R index b4ab8a5b98e..d9cb522a4e2 100644 --- a/opencga-client/src/main/R/R/Project-methods.R +++ b/opencga-client/src/main/R/R/Project-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Sample-methods.R b/opencga-client/src/main/R/R/Sample-methods.R index 89b2d7b5876..8a8d00d9796 100644 --- a/opencga-client/src/main/R/R/Sample-methods.R +++ b/opencga-client/src/main/R/R/Sample-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("sampleClient", "OpencgaR", function(OpencgaR, members, sample, samples, annotationSet, endpointName, params=NULL, ...) { +setMethod("sampleClient", "OpencgaR", function(OpencgaR, annotationSet, sample, samples, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/samples/acl/{members}/update: @@ -98,7 +98,7 @@ setMethod("sampleClient", "OpencgaR", function(OpencgaR, members, sample, sample #' @section Endpoint /{apiVersion}/samples/distinct: #' Sample distinct method. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list sample IDs up to a maximum of 100. + #' @param id Comma separated list sample IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list sample UUIDs up to a maximum of 100. #' @param somatic Somatic sample. #' @param individualId Individual ID or UUID. @@ -115,7 +115,7 @@ setMethod("sampleClient", "OpencgaR", function(OpencgaR, members, sample, sample #' @param collectionFrom Collection from. #' @param collectionType Collection type. #' @param collectionMethod Collection method. - #' @param phenotypes Comma separated list of phenotype ids or names. + #' @param phenotypes Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param annotation Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. #' @param acl Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example: acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which user john has both WRITE and WRITE_ANNOTATIONS permissions. Only study owners or administrators can query by this field. . #' @param internalRgaStatus Index status of the sample for the Recessive Gene Analysis. Allowed values: ['NOT_INDEXED INDEXED INVALID_PERMISSIONS INVALID_METADATA INVALID'] @@ -157,7 +157,7 @@ setMethod("sampleClient", "OpencgaR", function(OpencgaR, members, sample, sample #' @param includeIndividual Include Individual object as an attribute. #' @param flattenAnnotations Flatten the annotations?. #' @param study Study [[user@]project:]study where study and project can be either the ID or UUID. - #' @param id Comma separated list sample IDs up to a maximum of 100. + #' @param id Comma separated list sample IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param uuid Comma separated list sample UUIDs up to a maximum of 100. #' @param somatic Somatic sample. #' @param individualId Individual ID or UUID. @@ -174,7 +174,7 @@ setMethod("sampleClient", "OpencgaR", function(OpencgaR, members, sample, sample #' @param collectionFrom Collection from. #' @param collectionType Collection type. #' @param collectionMethod Collection method. - #' @param phenotypes Comma separated list of phenotype ids or names. + #' @param phenotypes Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. #' @param annotation Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. #' @param acl Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example: acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which user john has both WRITE and WRITE_ANNOTATIONS permissions. Only study owners or administrators can query by this field. . #' @param internalRgaStatus Index status of the sample for the Recessive Gene Analysis. Allowed values: ['NOT_INDEXED INDEXED INVALID_PERMISSIONS INVALID_METADATA INVALID'] diff --git a/opencga-client/src/main/R/R/Study-methods.R b/opencga-client/src/main/R/R/Study-methods.R index 754fa677dea..84227b71b68 100644 --- a/opencga-client/src/main/R/R/Study-methods.R +++ b/opencga-client/src/main/R/R/Study-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -46,7 +46,7 @@ #' [*]: Required parameter #' @export -setMethod("studyClient", "OpencgaR", function(OpencgaR, members, variableSet, studies, group, study, templateId, endpointName, params=NULL, ...) { +setMethod("studyClient", "OpencgaR", function(OpencgaR, variableSet, studies, members, group, study, templateId, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/studies/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/User-methods.R b/opencga-client/src/main/R/R/User-methods.R index 7fb54a32ff1..51b6157fe7a 100644 --- a/opencga-client/src/main/R/R/User-methods.R +++ b/opencga-client/src/main/R/R/User-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("userClient", "OpencgaR", function(OpencgaR, user, filterId, users, endpointName, params=NULL, ...) { +setMethod("userClient", "OpencgaR", function(OpencgaR, filterId, users, user, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/users/login: diff --git a/opencga-client/src/main/R/R/Variant-methods.R b/opencga-client/src/main/R/R/Variant-methods.R index 0b7a706cb8f..6d17848726b 100644 --- a/opencga-client/src/main/R/R/Variant-methods.R +++ b/opencga-client/src/main/R/R/Variant-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-08-30 +# Autogenerated on: 2023-09-01 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java index 2a375bb7b83..df137812b2f 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java index 08257cc1a1a..759e68f1b90 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java @@ -40,7 +40,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java index 32ab712003e..22eeeca0ccd 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java @@ -51,7 +51,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -127,10 +127,12 @@ public RestResponse create(ClinicalAnalysisCreateParams data, * @param field Comma separated list of fields for which to obtain the distinct values. * @param params Map containing any of the following optional parameters. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of Clinical Analysis IDs up to a maximum of 100. + * id: Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. * type: Clinical Analysis type. - * disorder: Clinical Analysis disorder. + * disorder: Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * files: Clinical Analysis files. * sample: Sample associated to the proband or any member of a family. * individual: Proband or any member of a family. @@ -166,11 +168,13 @@ public RestResponse distinct(String field, ObjectMap params) throws C * @param field Comma separated list of fields for which to obtain the distinct values. * @param params Map containing any of the following optional parameters. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of Interpretation IDs up to a maximum of 100. + * id: Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list of Interpretation UUIDs up to a maximum of 100. * clinicalAnalysisId: Clinical Analysis id. * analystId: Analyst ID. - * methodName: Interpretation method name. + * methodName: Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' + * e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * panels: Interpretation panels. * primaryFindings: Interpretation primary findings. * secondaryFindings: Interpretation secondary findings. @@ -197,11 +201,13 @@ public RestResponse distinctInterpretation(String field, ObjectMap pa * skip: Number of results to skip. * sort: Sort the results. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of Interpretation IDs up to a maximum of 100. + * id: Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list of Interpretation UUIDs up to a maximum of 100. * clinicalAnalysisId: Clinical Analysis id. * analystId: Analyst ID. - * methodName: Interpretation method name. + * methodName: Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' + * e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * panels: Interpretation panels. * primaryFindings: Interpretation primary findings. * secondaryFindings: Interpretation secondary findings. @@ -614,10 +620,12 @@ public RestResponse summaryRgaVariant(ObjectMap params * skip: Number of results to skip. * count: Get the total number of results matching the query. Deactivated by default. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of Clinical Analysis IDs up to a maximum of 100. + * id: Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. * type: Clinical Analysis type. - * disorder: Clinical Analysis disorder. + * disorder: Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * files: Clinical Analysis files. * sample: Sample associated to the proband or any member of a family. * individual: Proband or any member of a family. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java index 547601b9329..4afa30f7993 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java @@ -37,7 +37,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -144,8 +144,10 @@ public RestResponse create(CohortCreateParams data, ObjectMap params) th * @param field Comma separated list of fields for which to obtain the distinct values. * @param params Map containing any of the following optional parameters. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of cohort IDs up to a maximum of 100. - * name: Comma separated list of cohort names up to a maximum of 100. + * id: Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * name: Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions using the operator + * '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list of cohort IDs up to a maximum of 100. * type: Cohort type. * creationDate: creationDate. @@ -182,7 +184,8 @@ public RestResponse distinct(String field, ObjectMap params) throws Clie * modificationDate: Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * internalStatus: Filter by internal status. * status: Filter by status. - * phenotypes: Comma separated list of phenotype ids or names. + * phenotypes: Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * annotation: Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit * http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. * acl: Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example: @@ -210,8 +213,10 @@ public RestResponse generate(CohortGenerateParams data, ObjectMap params * count: Get the total number of results matching the query. Deactivated by default. * flattenAnnotations: Flatten the annotations?. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of cohort IDs up to a maximum of 100. - * name: Comma separated list of cohort names up to a maximum of 100. + * id: Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * name: Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions using the operator + * '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list of cohort IDs up to a maximum of 100. * type: Cohort type. * creationDate: creationDate. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java index ad5ea1a7047..ec146dbae49 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java @@ -35,7 +35,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -93,17 +93,27 @@ public RestResponse create(PanelCreateParams data, ObjectMap params) thro * @param field Comma separated list of fields for which to obtain the distinct values. * @param params Map containing any of the following optional parameters. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of panel IDs up to a maximum of 100. + * id: Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list of panel UUIDs up to a maximum of 100. - * name: Comma separated list of panel names up to a maximum of 100. + * name: Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions using the operator + * '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * internalStatus: Filter by internal status. - * disorders: Comma separated list of disorder ids or names. - * variants: Comma separated list of variant ids. - * genes: Comma separated list of gene ids. + * disorders: Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic regular + * expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case + * insensitive search. + * variants: Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * genes: Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' + * e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * source: Comma separated list of source ids or names. - * regions: Comma separated list of regions. - * categories: Comma separated list of category names. - * tags: Panel tags. + * regions: Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' + * e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * categories: Comma separated list of category names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * tags: Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + * sensitive, '~/value/i' for case insensitive search. * deleted: Boolean to retrieve deleted entries. * status: Filter by status. * creationDate: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. @@ -149,17 +159,27 @@ public RestResponse importPanels(PanelImportParams data, ObjectMap params) * skip: Number of results to skip. * count: Get the total number of results matching the query. Deactivated by default. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of panel IDs up to a maximum of 100. + * id: Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list of panel UUIDs up to a maximum of 100. - * name: Comma separated list of panel names up to a maximum of 100. + * name: Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions using the operator + * '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * internalStatus: Filter by internal status. - * disorders: Comma separated list of disorder ids or names. - * variants: Comma separated list of variant ids. - * genes: Comma separated list of gene ids. + * disorders: Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic regular + * expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case + * insensitive search. + * variants: Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * genes: Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' + * e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * source: Comma separated list of source ids or names. - * regions: Comma separated list of regions. - * categories: Comma separated list of category names. - * tags: Panel tags. + * regions: Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' + * e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * categories: Comma separated list of category names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * tags: Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + * sensitive, '~/value/i' for case insensitive search. * deleted: Boolean to retrieve deleted entries. * status: Filter by status. * creationDate: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java index d113cbdaf09..cbd554fe8d4 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -145,14 +145,18 @@ public RestResponse create(FamilyCreateParams data, ObjectMap params) th * @param field Comma separated list of fields for which to obtain the distinct values. * @param params Map containing any of the following optional parameters. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list family IDs up to a maximum of 100. - * name: Comma separated list family names up to a maximum of 100. + * id: Comma separated list family IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * name: Comma separated list family names up to a maximum of 100. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list family UUIDs up to a maximum of 100. * members: Comma separated list of family members. * expectedSize: Expected size of the family (number of members). * samples: Comma separated list of member's samples. - * phenotypes: Comma separated list of phenotype ids or names. - * disorders: Comma separated list of disorder ids or names. + * phenotypes: Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * disorders: Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * creationDate: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * modificationDate: Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * deleted: Boolean to retrieve deleted entries. @@ -184,14 +188,18 @@ public RestResponse distinct(String field, ObjectMap params) throws Clie * count: Get the total number of results matching the query. Deactivated by default. * flattenAnnotations: Flatten the annotations?. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list family IDs up to a maximum of 100. - * name: Comma separated list family names up to a maximum of 100. + * id: Comma separated list family IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * name: Comma separated list family names up to a maximum of 100. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list family UUIDs up to a maximum of 100. * members: Comma separated list of family members. * expectedSize: Expected size of the family (number of members). * samples: Comma separated list of member's samples. - * phenotypes: Comma separated list of phenotype ids or names. - * disorders: Comma separated list of disorder ids or names. + * phenotypes: Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * disorders: Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * creationDate: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * modificationDate: Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * deleted: Boolean to retrieve deleted entries. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java index 72be6ed305b..fc31ad2bec2 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java @@ -43,7 +43,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -164,11 +164,15 @@ public RestResponse create(FileCreateParams data, ObjectMap params) throws * @param field Comma separated list of fields for which to obtain the distinct values. * @param params Map containing any of the following optional parameters. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of file IDs up to a maximum of 100. + * id: Comma separated list of file IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list file UUIDs up to a maximum of 100. - * name: Comma separated list of file names. - * path: Comma separated list of paths. - * uri: Comma separated list of uris. + * name: Comma separated list of file names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' + * e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * path: Comma separated list of paths. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. + * uri: Comma separated list of uris. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * type: File type, either FILE or DIRECTORY. * bioformat: Comma separated Bioformat values. For existing Bioformats see files/bioformats. * format: Comma separated Format values. For existing Formats see files/formats. @@ -181,7 +185,8 @@ public RestResponse create(FileCreateParams data, ObjectMap params) throws * creationDate: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * modificationDate: Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * description: Description. - * tags: Tags. + * tags: Tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + * sensitive, '~/value/i' for case insensitive search. * size: File size. * sampleIds: Comma separated list sample IDs or UUIDs up to a maximum of 100. * jobId: Job ID that created the file(s) or folder(s). @@ -290,11 +295,15 @@ public RestResponse runPostlink(PostLinkToolParams data, ObjectMap params) * count: Get the total number of results matching the query. Deactivated by default. * flattenAnnotations: Boolean indicating to flatten the annotations. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list of file IDs up to a maximum of 100. + * id: Comma separated list of file IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list file UUIDs up to a maximum of 100. - * name: Comma separated list of file names. - * path: Comma separated list of paths. - * uri: Comma separated list of uris. + * name: Comma separated list of file names. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' + * e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * path: Comma separated list of paths. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. + * uri: Comma separated list of uris. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * type: File type, either FILE or DIRECTORY. * bioformat: Comma separated Bioformat values. For existing Bioformats see files/bioformats. * format: Comma separated Format values. For existing Formats see files/formats. @@ -307,7 +316,8 @@ public RestResponse runPostlink(PostLinkToolParams data, ObjectMap params) * creationDate: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * modificationDate: Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * description: Description. - * tags: Tags. + * tags: Tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + * sensitive, '~/value/i' for case insensitive search. * size: File size. * sampleIds: Comma separated list sample IDs or UUIDs up to a maximum of 100. * jobId: Job ID that created the file(s) or folder(s). diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java index fbb84f972a4..b0afdac763a 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java @@ -27,7 +27,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java index 5803d125e54..27a9af45ed5 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -153,20 +153,27 @@ public RestResponse create(IndividualCreateParams data, ObjectMap pa * @param field Comma separated list of fields for which to obtain the distinct values. * @param params Map containing any of the following optional parameters. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list individual IDs up to a maximum of 100. + * id: Comma separated list individual IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list individual UUIDs up to a maximum of 100. - * name: Comma separated list individual names up to a maximum of 100. + * name: Comma separated list individual names up to a maximum of 100. Also admits basic regular expressions using the operator + * '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * familyIds: Comma separated list of family ids the individuals may belong to. * father: Father ID, name or UUID. * mother: Mother ID, name or UUID. * samples: Sample ID, name or UUID. * sex: Individual sex. - * ethnicity: Individual ethnicity. + * ethnicity: Individual ethnicity. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * dateOfBirth: Individual date of birth. - * disorders: Comma separated list of disorder ids or names. - * phenotypes: Comma separated list of phenotype ids or names. - * populationName: Population name. - * populationSubpopulation: Subpopulation name. + * disorders: Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * phenotypes: Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * populationName: Population name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. + * populationSubpopulation: Subpopulation name. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * karyotypicSex: Individual karyotypic sex. * lifeStatus: Individual life status. * internalStatus: Filter by internal status. @@ -200,20 +207,27 @@ public RestResponse distinct(String field, ObjectMap params) throws Clie * count: Get the total number of results matching the query. Deactivated by default. * flattenAnnotations: Flatten the annotations?. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list individual IDs up to a maximum of 100. + * id: Comma separated list individual IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list individual UUIDs up to a maximum of 100. - * name: Comma separated list individual names up to a maximum of 100. + * name: Comma separated list individual names up to a maximum of 100. Also admits basic regular expressions using the operator + * '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * father: Father ID, name or UUID. * mother: Mother ID, name or UUID. * samples: Sample ID, name or UUID. * familyIds: Comma separated list of family ids the individuals may belong to. * sex: Individual sex. * dateOfBirth: Individual date of birth. - * ethnicity: Individual ethnicity. - * disorders: Comma separated list of disorder ids or names. - * phenotypes: Comma separated list of phenotype ids or names. - * populationName: Population name. - * populationSubpopulation: Subpopulation name. + * ethnicity: Individual ethnicity. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. + * disorders: Comma separated list of disorder ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * phenotypes: Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * populationName: Population name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. + * populationSubpopulation: Subpopulation name. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * karyotypicSex: Individual karyotypic sex. * lifeStatus: Individual life status. * internalStatus: Filter by internal status. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java index 27245d4011c..f880ed1d600 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java @@ -37,7 +37,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -120,9 +120,11 @@ public RestResponse create(JobCreateParams data, ObjectMap params) throws C * @param params Map containing any of the following optional parameters. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. * otherStudies: Flag indicating the entries being queried can belong to any related study, not just the primary one. - * id: Comma separated list of job IDs up to a maximum of 100. + * id: Comma separated list of job IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list of job UUIDs up to a maximum of 100. - * toolId: Tool ID executed by the job. + * toolId: Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * toolType: Tool type executed by the job [OPERATION, ANALYSIS]. * userId: User that created the job. * priority: Priority of the job. @@ -176,9 +178,11 @@ public RestResponse retry(JobRetryParams data, ObjectMap params) throws Cli * count: Get the total number of results matching the query. Deactivated by default. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. * otherStudies: Flag indicating the entries being queried can belong to any related study, not just the primary one. - * id: Comma separated list of job IDs up to a maximum of 100. + * id: Comma separated list of job IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list of job UUIDs up to a maximum of 100. - * toolId: Tool ID executed by the job. + * toolId: Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * toolType: Tool type executed by the job [OPERATION, ANALYSIS]. * userId: User that created the job. * priority: Priority of the job. @@ -211,7 +215,8 @@ public RestResponse search(ObjectMap params) throws ClientException { * internalStatus: Filter by internal status. * priority: Priority of the job. * userId: User that created the job. - * toolId: Tool ID executed by the job. + * toolId: Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * @return a RestResponse object. * @throws ClientException ClientException if there is any server error. */ diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java index c2c015b670d..15ca508dc41 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java @@ -28,7 +28,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java index 47aeec33622..fb3f13b0077 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java @@ -32,7 +32,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java index d2dd71bc2f3..5399ebea102 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -145,7 +145,8 @@ public RestResponse create(SampleCreateParams data, ObjectMap params) th * @param field Comma separated list of fields for which to obtain the distinct values. * @param params Map containing any of the following optional parameters. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list sample IDs up to a maximum of 100. + * id: Comma separated list sample IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list sample UUIDs up to a maximum of 100. * somatic: Somatic sample. * individualId: Individual ID or UUID. @@ -162,7 +163,8 @@ public RestResponse create(SampleCreateParams data, ObjectMap params) th * collectionFrom: Collection from. * collectionType: Collection type. * collectionMethod: Collection method. - * phenotypes: Comma separated list of phenotype ids or names. + * phenotypes: Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * annotation: Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit * http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. * acl: Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example: @@ -221,7 +223,8 @@ public RestResponse load(String file, ObjectMap params) throws ClientExc * includeIndividual: Include Individual object as an attribute. * flattenAnnotations: Flatten the annotations?. * study: Study [[user@]project:]study where study and project can be either the ID or UUID. - * id: Comma separated list sample IDs up to a maximum of 100. + * id: Comma separated list sample IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * uuid: Comma separated list sample UUIDs up to a maximum of 100. * somatic: Somatic sample. * individualId: Individual ID or UUID. @@ -238,7 +241,8 @@ public RestResponse load(String file, ObjectMap params) throws ClientExc * collectionFrom: Collection from. * collectionType: Collection type. * collectionMethod: Collection method. - * phenotypes: Comma separated list of phenotype ids or names. + * phenotypes: Comma separated list of phenotype ids or names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * annotation: Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit * http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. * acl: Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example: diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java index 53502e91c7e..f5cc56d0d9c 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java @@ -45,7 +45,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java index eda89cb9228..e6c291036f5 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java index 0d25391978a..0e88f0a112c 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java @@ -62,7 +62,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java index ae6bef9d18d..e0e2f076484 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java @@ -50,7 +50,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-08-30 +* Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Admin.js b/opencga-client/src/main/javascript/Admin.js index 26d6d454012..d372e15a01c 100644 --- a/opencga-client/src/main/javascript/Admin.js +++ b/opencga-client/src/main/javascript/Admin.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Alignment.js b/opencga-client/src/main/javascript/Alignment.js index 33aa92db017..7a1e4809128 100644 --- a/opencga-client/src/main/javascript/Alignment.js +++ b/opencga-client/src/main/javascript/Alignment.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/ClinicalAnalysis.js b/opencga-client/src/main/javascript/ClinicalAnalysis.js index 4434d811346..1054e70f292 100644 --- a/opencga-client/src/main/javascript/ClinicalAnalysis.js +++ b/opencga-client/src/main/javascript/ClinicalAnalysis.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -76,10 +76,12 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of Clinical Analysis IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular + * expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. * @param {String} [params.type] - Clinical Analysis type. - * @param {String} [params.disorder] - Clinical Analysis disorder. + * @param {String} [params.disorder] - Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.files] - Clinical Analysis files. * @param {String} [params.sample] - Sample associated to the proband or any member of a family. * @param {String} [params.individual] - Proband or any member of a family. @@ -112,11 +114,13 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of Interpretation IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of Interpretation UUIDs up to a maximum of 100. * @param {String} [params.clinicalAnalysisId] - Clinical Analysis id. * @param {String} [params.analystId] - Analyst ID. - * @param {String} [params.methodName] - Interpretation method name. + * @param {String} [params.methodName] - Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.panels] - Interpretation panels. * @param {String} [params.primaryFindings] - Interpretation primary findings. * @param {String} [params.secondaryFindings] - Interpretation secondary findings. @@ -140,11 +144,13 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @param {Number} [params.skip] - Number of results to skip. * @param {Boolean} [params.sort] - Sort the results. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of Interpretation IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of Interpretation UUIDs up to a maximum of 100. * @param {String} [params.clinicalAnalysisId] - Clinical Analysis id. * @param {String} [params.analystId] - Analyst ID. - * @param {String} [params.methodName] - Interpretation method name. + * @param {String} [params.methodName] - Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.panels] - Interpretation panels. * @param {String} [params.primaryFindings] - Interpretation primary findings. * @param {String} [params.secondaryFindings] - Interpretation secondary findings. @@ -513,10 +519,12 @@ export default class ClinicalAnalysis extends OpenCGAParentClass { * @param {Boolean} [params.count = "false"] - Get the total number of results matching the query. Deactivated by default. The default * value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of Clinical Analysis IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular + * expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. * @param {String} [params.type] - Clinical Analysis type. - * @param {String} [params.disorder] - Clinical Analysis disorder. + * @param {String} [params.disorder] - Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.files] - Clinical Analysis files. * @param {String} [params.sample] - Sample associated to the proband or any member of a family. * @param {String} [params.individual] - Proband or any member of a family. diff --git a/opencga-client/src/main/javascript/Cohort.js b/opencga-client/src/main/javascript/Cohort.js index cb53c5278a3..11d9d5906f6 100644 --- a/opencga-client/src/main/javascript/Cohort.js +++ b/opencga-client/src/main/javascript/Cohort.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -101,8 +101,10 @@ export default class Cohort extends OpenCGAParentClass { * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of cohort IDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list of cohort names up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.name] - Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of cohort IDs up to a maximum of 100. * @param {String} [params.type] - Cohort type. * @param {String} [params.creationDate] - creationDate. @@ -135,7 +137,8 @@ export default class Cohort extends OpenCGAParentClass { * @param {String} [params.modificationDate] - Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.internalStatus] - Filter by internal status. * @param {String} [params.status] - Filter by status. - * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. + * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.annotation] - Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit * http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. * @param {String} [params.acl] - Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. @@ -161,8 +164,10 @@ export default class Cohort extends OpenCGAParentClass { * value is false. * @param {Boolean} [params.flattenAnnotations = "false"] - Flatten the annotations?. The default value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of cohort IDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list of cohort names up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of cohort IDs up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.name] - Comma separated list of cohort names up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of cohort IDs up to a maximum of 100. * @param {String} [params.type] - Cohort type. * @param {String} [params.creationDate] - creationDate. diff --git a/opencga-client/src/main/javascript/DiseasePanel.js b/opencga-client/src/main/javascript/DiseasePanel.js index a4bc253c0bd..1c427e0629f 100644 --- a/opencga-client/src/main/javascript/DiseasePanel.js +++ b/opencga-client/src/main/javascript/DiseasePanel.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -62,17 +62,27 @@ export default class DiseasePanel extends OpenCGAParentClass { * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of panel IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of panel UUIDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list of panel names up to a maximum of 100. + * @param {String} [params.name] - Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.internalStatus] - Filter by internal status. - * @param {String} [params.disorders] - Comma separated list of disorder ids or names. - * @param {String} [params.variants] - Comma separated list of variant ids. - * @param {String} [params.genes] - Comma separated list of gene ids. + * @param {String} [params.disorders] - Comma separated list of disorder ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic + * regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive + * search. + * @param {String} [params.variants] - Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.genes] - Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.source] - Comma separated list of source ids or names. - * @param {String} [params.regions] - Comma separated list of regions. - * @param {String} [params.categories] - Comma separated list of category names. - * @param {String} [params.tags] - Panel tags. + * @param {String} [params.regions] - Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.categories] - Comma separated list of category names. Also admits basic regular expressions using the operator + * '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.tags] - Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {Boolean} [params.deleted = "false"] - Boolean to retrieve deleted entries. The default value is false. * @param {String} [params.status] - Filter by status. * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. @@ -112,17 +122,27 @@ export default class DiseasePanel extends OpenCGAParentClass { * @param {Boolean} [params.count = "false"] - Get the total number of results matching the query. Deactivated by default. The default * value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of panel IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of panel IDs up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of panel UUIDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list of panel names up to a maximum of 100. + * @param {String} [params.name] - Comma separated list of panel names up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.internalStatus] - Filter by internal status. - * @param {String} [params.disorders] - Comma separated list of disorder ids or names. - * @param {String} [params.variants] - Comma separated list of variant ids. - * @param {String} [params.genes] - Comma separated list of gene ids. + * @param {String} [params.disorders] - Comma separated list of disorder ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.. Also admits basic + * regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive + * search. + * @param {String} [params.variants] - Comma separated list of variant ids. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.genes] - Comma separated list of gene ids. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.source] - Comma separated list of source ids or names. - * @param {String} [params.regions] - Comma separated list of regions. - * @param {String} [params.categories] - Comma separated list of category names. - * @param {String} [params.tags] - Panel tags. + * @param {String} [params.regions] - Comma separated list of regions. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.categories] - Comma separated list of category names. Also admits basic regular expressions using the operator + * '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.tags] - Panel tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. + * '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {Boolean} [params.deleted = "false"] - Boolean to retrieve deleted entries. The default value is false. * @param {String} [params.status] - Filter by status. * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. diff --git a/opencga-client/src/main/javascript/Family.js b/opencga-client/src/main/javascript/Family.js index e971b3b2e81..90d31e15443 100644 --- a/opencga-client/src/main/javascript/Family.js +++ b/opencga-client/src/main/javascript/Family.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -104,14 +104,18 @@ export default class Family extends OpenCGAParentClass { * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list family IDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list family names up to a maximum of 100. + * @param {String} [params.id] - Comma separated list family IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.name] - Comma separated list family names up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list family UUIDs up to a maximum of 100. * @param {String} [params.members] - Comma separated list of family members. * @param {Number} [params.expectedSize] - Expected size of the family (number of members). * @param {String} [params.samples] - Comma separated list of member's samples. - * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. - * @param {String} [params.disorders] - Comma separated list of disorder ids or names. + * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.disorders] - Comma separated list of disorder ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.modificationDate] - Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {Boolean} [params.deleted = "false"] - Boolean to retrieve deleted entries. The default value is false. @@ -140,14 +144,18 @@ export default class Family extends OpenCGAParentClass { * value is false. * @param {Boolean} [params.flattenAnnotations = "false"] - Flatten the annotations?. The default value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list family IDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list family names up to a maximum of 100. + * @param {String} [params.id] - Comma separated list family IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.name] - Comma separated list family names up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list family UUIDs up to a maximum of 100. * @param {String} [params.members] - Comma separated list of family members. * @param {Number} [params.expectedSize] - Expected size of the family (number of members). * @param {String} [params.samples] - Comma separated list of member's samples. - * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. - * @param {String} [params.disorders] - Comma separated list of disorder ids or names. + * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.disorders] - Comma separated list of disorder ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.modificationDate] - Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {Boolean} [params.deleted = "false"] - Boolean to retrieve deleted entries. The default value is false. diff --git a/opencga-client/src/main/javascript/File.js b/opencga-client/src/main/javascript/File.js index b3219c4f08a..d5678f46153 100644 --- a/opencga-client/src/main/javascript/File.js +++ b/opencga-client/src/main/javascript/File.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -112,11 +112,15 @@ export default class File extends OpenCGAParentClass { * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of file IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of file IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list file UUIDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list of file names. - * @param {String} [params.path] - Comma separated list of paths. - * @param {String} [params.uri] - Comma separated list of uris. + * @param {String} [params.name] - Comma separated list of file names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.path] - Comma separated list of paths. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.uri] - Comma separated list of uris. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.type] - File type, either FILE or DIRECTORY. * @param {String} [params.bioformat] - Comma separated Bioformat values. For existing Bioformats see files/bioformats. * @param {String} [params.format] - Comma separated Format values. For existing Formats see files/formats. @@ -129,7 +133,8 @@ export default class File extends OpenCGAParentClass { * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.modificationDate] - Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.description] - Description. - * @param {String} [params.tags] - Tags. + * @param {String} [params.tags] - Tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' + * for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.size] - File size. * @param {String} [params.sampleIds] - Comma separated list sample IDs or UUIDs up to a maximum of 100. * @param {String} [params.jobId] - Job ID that created the file(s) or folder(s). @@ -220,11 +225,15 @@ export default class File extends OpenCGAParentClass { * value is false. * @param {Boolean} [params.flattenAnnotations = "false"] - Boolean indicating to flatten the annotations. The default value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list of file IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of file IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list file UUIDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list of file names. - * @param {String} [params.path] - Comma separated list of paths. - * @param {String} [params.uri] - Comma separated list of uris. + * @param {String} [params.name] - Comma separated list of file names. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.path] - Comma separated list of paths. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.uri] - Comma separated list of uris. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.type] - File type, either FILE or DIRECTORY. * @param {String} [params.bioformat] - Comma separated Bioformat values. For existing Bioformats see files/bioformats. * @param {String} [params.format] - Comma separated Format values. For existing Formats see files/formats. @@ -237,7 +246,8 @@ export default class File extends OpenCGAParentClass { * @param {String} [params.creationDate] - Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.modificationDate] - Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. * @param {String} [params.description] - Description. - * @param {String} [params.tags] - Tags. + * @param {String} [params.tags] - Tags. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' + * for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.size] - File size. * @param {String} [params.sampleIds] - Comma separated list sample IDs or UUIDs up to a maximum of 100. * @param {String} [params.jobId] - Job ID that created the file(s) or folder(s). diff --git a/opencga-client/src/main/javascript/GA4GH.js b/opencga-client/src/main/javascript/GA4GH.js index ec01beb21de..52d93be35f7 100644 --- a/opencga-client/src/main/javascript/GA4GH.js +++ b/opencga-client/src/main/javascript/GA4GH.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Individual.js b/opencga-client/src/main/javascript/Individual.js index 71eb45dbafd..b66f0fc8aee 100644 --- a/opencga-client/src/main/javascript/Individual.js +++ b/opencga-client/src/main/javascript/Individual.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -111,20 +111,27 @@ export default class Individual extends OpenCGAParentClass { * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list individual IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list individual IDs up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list individual UUIDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list individual names up to a maximum of 100. + * @param {String} [params.name] - Comma separated list individual names up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.familyIds] - Comma separated list of family ids the individuals may belong to. * @param {String} [params.father] - Father ID, name or UUID. * @param {String} [params.mother] - Mother ID, name or UUID. * @param {String} [params.samples] - Sample ID, name or UUID. * @param {String} [params.sex] - Individual sex. - * @param {String} [params.ethnicity] - Individual ethnicity. + * @param {String} [params.ethnicity] - Individual ethnicity. Also admits basic regular expressions using the operator '~', i.e. '~{perl- + * regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.dateOfBirth] - Individual date of birth. - * @param {String} [params.disorders] - Comma separated list of disorder ids or names. - * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. - * @param {String} [params.populationName] - Population name. - * @param {String} [params.populationSubpopulation] - Subpopulation name. + * @param {String} [params.disorders] - Comma separated list of disorder ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.populationName] - Population name. Also admits basic regular expressions using the operator '~', i.e. '~{perl- + * regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.populationSubpopulation] - Subpopulation name. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.karyotypicSex] - Individual karyotypic sex. * @param {String} [params.lifeStatus] - Individual life status. * @param {String} [params.internalStatus] - Filter by internal status. @@ -155,20 +162,27 @@ export default class Individual extends OpenCGAParentClass { * value is false. * @param {Boolean} [params.flattenAnnotations = "false"] - Flatten the annotations?. The default value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list individual IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list individual IDs up to a maximum of 100. Also admits basic regular expressions using + * the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list individual UUIDs up to a maximum of 100. - * @param {String} [params.name] - Comma separated list individual names up to a maximum of 100. + * @param {String} [params.name] - Comma separated list individual names up to a maximum of 100. Also admits basic regular expressions + * using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.father] - Father ID, name or UUID. * @param {String} [params.mother] - Mother ID, name or UUID. * @param {String} [params.samples] - Sample ID, name or UUID. * @param {String} [params.familyIds] - Comma separated list of family ids the individuals may belong to. * @param {String} [params.sex] - Individual sex. * @param {String} [params.dateOfBirth] - Individual date of birth. - * @param {String} [params.ethnicity] - Individual ethnicity. - * @param {String} [params.disorders] - Comma separated list of disorder ids or names. - * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. - * @param {String} [params.populationName] - Population name. - * @param {String} [params.populationSubpopulation] - Subpopulation name. + * @param {String} [params.ethnicity] - Individual ethnicity. Also admits basic regular expressions using the operator '~', i.e. '~{perl- + * regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.disorders] - Comma separated list of disorder ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.populationName] - Population name. Also admits basic regular expressions using the operator '~', i.e. '~{perl- + * regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. + * @param {String} [params.populationSubpopulation] - Subpopulation name. Also admits basic regular expressions using the operator '~', + * i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.karyotypicSex] - Individual karyotypic sex. * @param {String} [params.lifeStatus] - Individual life status. * @param {String} [params.internalStatus] - Filter by internal status. diff --git a/opencga-client/src/main/javascript/Job.js b/opencga-client/src/main/javascript/Job.js index 1e1cc91bc52..8128ce9db7d 100644 --- a/opencga-client/src/main/javascript/Job.js +++ b/opencga-client/src/main/javascript/Job.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -85,9 +85,11 @@ export default class Job extends OpenCGAParentClass { * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. * @param {Boolean} [params.otherStudies = "false"] - Flag indicating the entries being queried can belong to any related study, not just * the primary one. The default value is false. - * @param {String} [params.id] - Comma separated list of job IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of job IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of job UUIDs up to a maximum of 100. - * @param {String} [params.toolId] - Tool ID executed by the job. + * @param {String} [params.toolId] - Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.toolType] - Tool type executed by the job [OPERATION, ANALYSIS]. * @param {String} [params.userId] - User that created the job. * @param {String} [params.priority] - Priority of the job. @@ -136,9 +138,11 @@ export default class Job extends OpenCGAParentClass { * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. * @param {Boolean} [params.otherStudies = "false"] - Flag indicating the entries being queried can belong to any related study, not just * the primary one. The default value is false. - * @param {String} [params.id] - Comma separated list of job IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list of job IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list of job UUIDs up to a maximum of 100. - * @param {String} [params.toolId] - Tool ID executed by the job. + * @param {String} [params.toolId] - Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.toolType] - Tool type executed by the job [OPERATION, ANALYSIS]. * @param {String} [params.userId] - User that created the job. * @param {String} [params.priority] - Priority of the job. @@ -168,7 +172,8 @@ export default class Job extends OpenCGAParentClass { * @param {String} [params.internalStatus] - Filter by internal status. * @param {String} [params.priority] - Priority of the job. * @param {String} [params.userId] - User that created the job. - * @param {String} [params.toolId] - Tool ID executed by the job. + * @param {String} [params.toolId] - Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. + * '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @returns {Promise} Promise object in the form of RestResponse instance. */ top(params) { diff --git a/opencga-client/src/main/javascript/Meta.js b/opencga-client/src/main/javascript/Meta.js index 24dfe87c63d..96fcc5b6d68 100644 --- a/opencga-client/src/main/javascript/Meta.js +++ b/opencga-client/src/main/javascript/Meta.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Project.js b/opencga-client/src/main/javascript/Project.js index e240c25cb46..8c4e02f956e 100644 --- a/opencga-client/src/main/javascript/Project.js +++ b/opencga-client/src/main/javascript/Project.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Sample.js b/opencga-client/src/main/javascript/Sample.js index 03c6a5b8d8f..74c71a5206f 100644 --- a/opencga-client/src/main/javascript/Sample.js +++ b/opencga-client/src/main/javascript/Sample.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -103,7 +103,8 @@ export default class Sample extends OpenCGAParentClass { * @param {String} field - Comma separated list of fields for which to obtain the distinct values. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list sample IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list sample IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list sample UUIDs up to a maximum of 100. * @param {Boolean} [params.somatic] - Somatic sample. * @param {String} [params.individualId] - Individual ID or UUID. @@ -120,7 +121,8 @@ export default class Sample extends OpenCGAParentClass { * @param {String} [params.collectionFrom] - Collection from. * @param {String} [params.collectionType] - Collection type. * @param {String} [params.collectionMethod] - Collection method. - * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. + * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.annotation] - Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit * http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. * @param {String} [params.acl] - Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. @@ -173,7 +175,8 @@ export default class Sample extends OpenCGAParentClass { * @param {Boolean} [params.includeIndividual = "false"] - Include Individual object as an attribute. The default value is false. * @param {Boolean} [params.flattenAnnotations = "false"] - Flatten the annotations?. The default value is false. * @param {String} [params.study] - Study [[user@]project:]study where study and project can be either the ID or UUID. - * @param {String} [params.id] - Comma separated list sample IDs up to a maximum of 100. + * @param {String} [params.id] - Comma separated list sample IDs up to a maximum of 100. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.uuid] - Comma separated list sample UUIDs up to a maximum of 100. * @param {Boolean} [params.somatic] - Somatic sample. * @param {String} [params.individualId] - Individual ID or UUID. @@ -190,7 +193,8 @@ export default class Sample extends OpenCGAParentClass { * @param {String} [params.collectionFrom] - Collection from. * @param {String} [params.collectionType] - Collection type. * @param {String} [params.collectionMethod] - Collection method. - * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. + * @param {String} [params.phenotypes] - Comma separated list of phenotype ids or names. Also admits basic regular expressions using the + * operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search. * @param {String} [params.annotation] - Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit * http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. * @param {String} [params.acl] - Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. diff --git a/opencga-client/src/main/javascript/Study.js b/opencga-client/src/main/javascript/Study.js index e99e8c7606b..54186dac4ec 100644 --- a/opencga-client/src/main/javascript/Study.js +++ b/opencga-client/src/main/javascript/Study.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/User.js b/opencga-client/src/main/javascript/User.js index bfed2a7bfec..ac91b91b891 100644 --- a/opencga-client/src/main/javascript/User.js +++ b/opencga-client/src/main/javascript/User.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Variant.js b/opencga-client/src/main/javascript/Variant.js index ae9365d5448..27eb9763570 100644 --- a/opencga-client/src/main/javascript/Variant.js +++ b/opencga-client/src/main/javascript/Variant.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/VariantOperation.js b/opencga-client/src/main/javascript/VariantOperation.js index f9837f69e25..192a736a775 100644 --- a/opencga-client/src/main/javascript/VariantOperation.js +++ b/opencga-client/src/main/javascript/VariantOperation.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-08-30 + * Autogenerated on: 2023-09-01 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py index e982694d126..2a5439b0d00 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py index b94f350449a..012e5296968 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py index ca4e1438978..6bd79233875 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -86,11 +86,16 @@ def distinct(self, field, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list of Clinical Analysis IDs up to a - maximum of 100. + maximum of 100. Also admits basic regular expressions using the + operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + sensitive, '~/value/i' for case insensitive search. :param str uuid: Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. :param str type: Clinical Analysis type. - :param str disorder: Clinical Analysis disorder. + :param str disorder: Clinical Analysis disorder. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str files: Clinical Analysis files. :param str sample: Sample associated to the proband or any member of a family. @@ -133,12 +138,17 @@ def distinct_interpretation(self, field, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list of Interpretation IDs up to a - maximum of 100. + maximum of 100. Also admits basic regular expressions using the + operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + sensitive, '~/value/i' for case insensitive search. :param str uuid: Comma separated list of Interpretation UUIDs up to a maximum of 100. :param str clinical_analysis_id: Clinical Analysis id. :param str analyst_id: Analyst ID. - :param str method_name: Interpretation method name. + :param str method_name: Interpretation method name. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str panels: Interpretation panels. :param str primary_findings: Interpretation primary findings. :param str secondary_findings: Interpretation secondary findings. @@ -169,12 +179,17 @@ def search_interpretation(self, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list of Interpretation IDs up to a - maximum of 100. + maximum of 100. Also admits basic regular expressions using the + operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + sensitive, '~/value/i' for case insensitive search. :param str uuid: Comma separated list of Interpretation UUIDs up to a maximum of 100. :param str clinical_analysis_id: Clinical Analysis id. :param str analyst_id: Analyst ID. - :param str method_name: Interpretation method name. + :param str method_name: Interpretation method name. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str panels: Interpretation panels. :param str primary_findings: Interpretation primary findings. :param str secondary_findings: Interpretation secondary findings. @@ -606,11 +621,16 @@ def search(self, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list of Clinical Analysis IDs up to a - maximum of 100. + maximum of 100. Also admits basic regular expressions using the + operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + sensitive, '~/value/i' for case insensitive search. :param str uuid: Comma separated list of Clinical Analysis UUIDs up to a maximum of 100. :param str type: Clinical Analysis type. - :param str disorder: Clinical Analysis disorder. + :param str disorder: Clinical Analysis disorder. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str files: Clinical Analysis files. :param str sample: Sample associated to the proband or any member of a family. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py index fef4cafa48d..4b1be07e92a 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -121,9 +121,13 @@ def distinct(self, field, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list of cohort IDs up to a maximum of - 100. + 100. Also admits basic regular expressions using the operator '~', + i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' + for case insensitive search. :param str name: Comma separated list of cohort names up to a maximum - of 100. + of 100. Also admits basic regular expressions using the operator + '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, + '~/value/i' for case insensitive search. :param str uuid: Comma separated list of cohort IDs up to a maximum of 100. :param str type: Cohort type. @@ -166,6 +170,9 @@ def generate(self, data=None, **options): :param str internal_status: Filter by internal status. :param str status: Filter by status. :param str phenotypes: Comma separated list of phenotype ids or names. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str annotation: Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. @@ -200,9 +207,13 @@ def search(self, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list of cohort IDs up to a maximum of - 100. + 100. Also admits basic regular expressions using the operator '~', + i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' + for case insensitive search. :param str name: Comma separated list of cohort names up to a maximum - of 100. + of 100. Also admits basic regular expressions using the operator + '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, + '~/value/i' for case insensitive search. :param str uuid: Comma separated list of cohort IDs up to a maximum of 100. :param str type: Cohort type. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py index 8382900c307..a6fe0e432a5 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -67,19 +67,42 @@ def distinct(self, field, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list of panel IDs up to a maximum of - 100. + 100. Also admits basic regular expressions using the operator '~', + i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' + for case insensitive search. :param str uuid: Comma separated list of panel UUIDs up to a maximum of 100. :param str name: Comma separated list of panel names up to a maximum - of 100. + of 100. Also admits basic regular expressions using the operator + '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, + '~/value/i' for case insensitive search. :param str internal_status: Filter by internal status. :param str disorders: Comma separated list of disorder ids or names. - :param str variants: Comma separated list of variant ids. - :param str genes: Comma separated list of gene ids. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search.. Also admits basic regular expressions + using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + sensitive, '~/value/i' for case insensitive search. + :param str variants: Comma separated list of variant ids. Also admits + basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. + :param str genes: Comma separated list of gene ids. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str source: Comma separated list of source ids or names. - :param str regions: Comma separated list of regions. - :param str categories: Comma separated list of category names. - :param str tags: Panel tags. + :param str regions: Comma separated list of regions. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. + :param str categories: Comma separated list of category names. Also + admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. + :param str tags: Panel tags. Also admits basic regular expressions + using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + sensitive, '~/value/i' for case insensitive search. :param bool deleted: Boolean to retrieve deleted entries. :param str status: Filter by status. :param str creation_date: Creation date. Format: yyyyMMddHHmmss. @@ -133,19 +156,42 @@ def search(self, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list of panel IDs up to a maximum of - 100. + 100. Also admits basic regular expressions using the operator '~', + i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' + for case insensitive search. :param str uuid: Comma separated list of panel UUIDs up to a maximum of 100. :param str name: Comma separated list of panel names up to a maximum - of 100. + of 100. Also admits basic regular expressions using the operator + '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, + '~/value/i' for case insensitive search. :param str internal_status: Filter by internal status. :param str disorders: Comma separated list of disorder ids or names. - :param str variants: Comma separated list of variant ids. - :param str genes: Comma separated list of gene ids. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search.. Also admits basic regular expressions + using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + sensitive, '~/value/i' for case insensitive search. + :param str variants: Comma separated list of variant ids. Also admits + basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. + :param str genes: Comma separated list of gene ids. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str source: Comma separated list of source ids or names. - :param str regions: Comma separated list of regions. - :param str categories: Comma separated list of category names. - :param str tags: Panel tags. + :param str regions: Comma separated list of regions. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. + :param str categories: Comma separated list of category names. Also + admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. + :param str tags: Panel tags. Also admits basic regular expressions + using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + sensitive, '~/value/i' for case insensitive search. :param bool deleted: Boolean to retrieve deleted entries. :param str status: Filter by status. :param str creation_date: Creation date. Format: yyyyMMddHHmmss. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py index 0637f728a08..1d41d4a8488 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -124,8 +124,13 @@ def distinct(self, field, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list family IDs up to a maximum of 100. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str name: Comma separated list family names up to a maximum of - 100. + 100. Also admits basic regular expressions using the operator '~', + i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' + for case insensitive search. :param str uuid: Comma separated list family UUIDs up to a maximum of 100. :param str members: Comma separated list of family members. @@ -133,7 +138,13 @@ def distinct(self, field, **options): members). :param str samples: Comma separated list of member's samples. :param str phenotypes: Comma separated list of phenotype ids or names. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str disorders: Comma separated list of disorder ids or names. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str creation_date: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. :param str modification_date: Modification date. Format: @@ -174,8 +185,13 @@ def search(self, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list family IDs up to a maximum of 100. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str name: Comma separated list family names up to a maximum of - 100. + 100. Also admits basic regular expressions using the operator '~', + i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' + for case insensitive search. :param str uuid: Comma separated list family UUIDs up to a maximum of 100. :param str members: Comma separated list of family members. @@ -183,7 +199,13 @@ def search(self, **options): members). :param str samples: Comma separated list of member's samples. :param str phenotypes: Comma separated list of phenotype ids or names. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str disorders: Comma separated list of disorder ids or names. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str creation_date: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. :param str modification_date: Modification date. Format: diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py index 816cdf83c0b..e3a5a9b8988 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -129,12 +129,23 @@ def distinct(self, field, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list of file IDs up to a maximum of - 100. + 100. Also admits basic regular expressions using the operator '~', + i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' + for case insensitive search. :param str uuid: Comma separated list file UUIDs up to a maximum of 100. - :param str name: Comma separated list of file names. - :param str path: Comma separated list of paths. - :param str uri: Comma separated list of uris. + :param str name: Comma separated list of file names. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. + :param str path: Comma separated list of paths. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. + :param str uri: Comma separated list of uris. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str type: File type, either FILE or DIRECTORY. :param str bioformat: Comma separated Bioformat values. For existing Bioformats see files/bioformats. @@ -154,7 +165,9 @@ def distinct(self, field, **options): :param str modification_date: Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. :param str description: Description. - :param str tags: Tags. + :param str tags: Tags. Also admits basic regular expressions using the + operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + sensitive, '~/value/i' for case insensitive search. :param str size: File size. :param str sample_ids: Comma separated list sample IDs or UUIDs up to a maximum of 100. @@ -269,12 +282,23 @@ def search(self, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list of file IDs up to a maximum of - 100. + 100. Also admits basic regular expressions using the operator '~', + i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' + for case insensitive search. :param str uuid: Comma separated list file UUIDs up to a maximum of 100. - :param str name: Comma separated list of file names. - :param str path: Comma separated list of paths. - :param str uri: Comma separated list of uris. + :param str name: Comma separated list of file names. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. + :param str path: Comma separated list of paths. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. + :param str uri: Comma separated list of uris. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str type: File type, either FILE or DIRECTORY. :param str bioformat: Comma separated Bioformat values. For existing Bioformats see files/bioformats. @@ -294,7 +318,9 @@ def search(self, **options): :param str modification_date: Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805. :param str description: Description. - :param str tags: Tags. + :param str tags: Tags. Also admits basic regular expressions using the + operator '~', i.e. '~{perl-regex}' e.g. '~value' for case + sensitive, '~/value/i' for case insensitive search. :param str size: File size. :param str sample_ids: Comma separated list sample IDs or UUIDs up to a maximum of 100. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py index 6f62ec62786..0b077f4a7c6 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py index 3982f010208..e8213458d7b 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -132,23 +132,42 @@ def distinct(self, field, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list individual IDs up to a maximum of - 100. + 100. Also admits basic regular expressions using the operator '~', + i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' + for case insensitive search. :param str uuid: Comma separated list individual UUIDs up to a maximum of 100. :param str name: Comma separated list individual names up to a maximum - of 100. + of 100. Also admits basic regular expressions using the operator + '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, + '~/value/i' for case insensitive search. :param str family_ids: Comma separated list of family ids the individuals may belong to. :param str father: Father ID, name or UUID. :param str mother: Mother ID, name or UUID. :param str samples: Sample ID, name or UUID. :param str sex: Individual sex. - :param str ethnicity: Individual ethnicity. + :param str ethnicity: Individual ethnicity. Also admits basic regular + expressions using the operator '~', i.e. '~{perl-regex}' e.g. + '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str date_of_birth: Individual date of birth. :param str disorders: Comma separated list of disorder ids or names. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str phenotypes: Comma separated list of phenotype ids or names. - :param str population_name: Population name. - :param str population_subpopulation: Subpopulation name. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. + :param str population_name: Population name. Also admits basic regular + expressions using the operator '~', i.e. '~{perl-regex}' e.g. + '~value' for case sensitive, '~/value/i' for case insensitive + search. + :param str population_subpopulation: Subpopulation name. Also admits + basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str karyotypic_sex: Individual karyotypic sex. :param str life_status: Individual life status. :param str internal_status: Filter by internal status. @@ -191,11 +210,15 @@ def search(self, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list individual IDs up to a maximum of - 100. + 100. Also admits basic regular expressions using the operator '~', + i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' + for case insensitive search. :param str uuid: Comma separated list individual UUIDs up to a maximum of 100. :param str name: Comma separated list individual names up to a maximum - of 100. + of 100. Also admits basic regular expressions using the operator + '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, + '~/value/i' for case insensitive search. :param str father: Father ID, name or UUID. :param str mother: Mother ID, name or UUID. :param str samples: Sample ID, name or UUID. @@ -203,11 +226,26 @@ def search(self, **options): individuals may belong to. :param str sex: Individual sex. :param str date_of_birth: Individual date of birth. - :param str ethnicity: Individual ethnicity. + :param str ethnicity: Individual ethnicity. Also admits basic regular + expressions using the operator '~', i.e. '~{perl-regex}' e.g. + '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str disorders: Comma separated list of disorder ids or names. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str phenotypes: Comma separated list of phenotype ids or names. - :param str population_name: Population name. - :param str population_subpopulation: Subpopulation name. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. + :param str population_name: Population name. Also admits basic regular + expressions using the operator '~', i.e. '~{perl-regex}' e.g. + '~value' for case sensitive, '~/value/i' for case insensitive + search. + :param str population_subpopulation: Subpopulation name. Also admits + basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str karyotypic_sex: Individual karyotypic sex. :param str life_status: Individual life status. :param str internal_status: Filter by internal status. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py index 313cf0df796..fd4ac0a9386 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -92,9 +92,15 @@ def distinct(self, field, **options): :param bool other_studies: Flag indicating the entries being queried can belong to any related study, not just the primary one. :param str id: Comma separated list of job IDs up to a maximum of 100. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str uuid: Comma separated list of job UUIDs up to a maximum of 100. - :param str tool_id: Tool ID executed by the job. + :param str tool_id: Tool ID executed by the job. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str tool_type: Tool type executed by the job [OPERATION, ANALYSIS]. :param str user_id: User that created the job. @@ -157,9 +163,15 @@ def search(self, **options): :param bool other_studies: Flag indicating the entries being queried can belong to any related study, not just the primary one. :param str id: Comma separated list of job IDs up to a maximum of 100. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str uuid: Comma separated list of job UUIDs up to a maximum of 100. - :param str tool_id: Tool ID executed by the job. + :param str tool_id: Tool ID executed by the job. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. :param str tool_type: Tool type executed by the job [OPERATION, ANALYSIS]. :param str user_id: User that created the job. @@ -196,7 +208,10 @@ def top(self, **options): :param str internal_status: Filter by internal status. :param str priority: Priority of the job. :param str user_id: User that created the job. - :param str tool_id: Tool ID executed by the job. + :param str tool_id: Tool ID executed by the job. Also admits basic + regular expressions using the operator '~', i.e. '~{perl-regex}' + e.g. '~value' for case sensitive, '~/value/i' for case insensitive + search. """ return self._get(category='jobs', resource='top', **options) diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py index 189a5ab62ea..d9f841bb69d 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py index 0784b20594c..b5eac020645 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py index 258189685ef..dbd8d313d8a 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -122,6 +122,9 @@ def distinct(self, field, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list sample IDs up to a maximum of 100. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str uuid: Comma separated list sample UUIDs up to a maximum of 100. :param bool somatic: Somatic sample. @@ -143,6 +146,9 @@ def distinct(self, field, **options): :param str collection_type: Collection type. :param str collection_method: Collection method. :param str phenotypes: Comma separated list of phenotype ids or names. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str annotation: Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. @@ -215,6 +221,9 @@ def search(self, **options): :param str study: Study [[user@]project:]study where study and project can be either the ID or UUID. :param str id: Comma separated list sample IDs up to a maximum of 100. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str uuid: Comma separated list sample UUIDs up to a maximum of 100. :param bool somatic: Somatic sample. @@ -236,6 +245,9 @@ def search(self, **options): :param str collection_type: Collection type. :param str collection_method: Collection method. :param str phenotypes: Comma separated list of phenotype ids or names. + Also admits basic regular expressions using the operator '~', i.e. + '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for + case insensitive search. :param str annotation: Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py index 3726c1e0a3a..82c241c0eb2 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py index 80ac433566b..e7de326420c 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py index 32dfa804648..9e447940a11 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py index 4070484d219..87b0d72a7d2 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-08-30 + Autogenerated on: 2023-09-01 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java b/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java index a34b818924a..10cd2f3cdf2 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java @@ -68,9 +68,9 @@ public class ParamConstants { public static final String DISTINCT_FIELD_PARAM = "field"; public static final String DISTINCT_FIELD_DESCRIPTION = "Comma separated list of fields for which to obtain the distinct values"; public static final String PHENOTYPES_PARAM = "phenotypes"; - public static final String PHENOTYPES_DESCRIPTION = "Comma separated list of phenotype ids or names"; + public static final String PHENOTYPES_DESCRIPTION = "Comma separated list of phenotype ids or names" + REGEX_SUPPORT; public static final String DISORDERS_PARAM = "disorders"; - public static final String DISORDERS_DESCRIPTION = "Comma separated list of disorder ids or names"; + public static final String DISORDERS_DESCRIPTION = "Comma separated list of disorder ids or names" + REGEX_SUPPORT; public static final String BODY_PARAM = "body"; public static final String OVERWRITE = "overwrite"; @@ -320,8 +320,8 @@ public class ParamConstants { public static final String INDIVIDUAL_SEX_DESCRIPTION = "Individual sex"; public static final String INDIVIDUAL_ETHNICITY_DESCRIPTION = "Individual ethnicity" + REGEX_SUPPORT; public static final String INDIVIDUAL_DATE_OF_BIRTH_DESCRIPTION = "Individual date of birth"; - public static final String INDIVIDUAL_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION + REGEX_SUPPORT; - public static final String INDIVIDUAL_PHENOTYPES_DESCRIPTION = PHENOTYPES_DESCRIPTION + REGEX_SUPPORT; + public static final String INDIVIDUAL_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION; + public static final String INDIVIDUAL_PHENOTYPES_DESCRIPTION = PHENOTYPES_DESCRIPTION; public static final String INDIVIDUAL_POPULATION_NAME_DESCRIPTION = "Population name" + REGEX_SUPPORT; public static final String INDIVIDUAL_POPULATION_SUBPOPULATION_DESCRIPTION = "Subpopulation name" + REGEX_SUPPORT; public static final String INDIVIDUAL_KARYOTYPIC_SEX_DESCRIPTION = "Individual karyotypic sex"; @@ -360,8 +360,8 @@ public class ParamConstants { public static final String FAMILY_MEMBERS_DESCRIPTION = "Comma separated list of family members"; public static final String FAMILY_SAMPLES_DESCRIPTION = "Comma separated list of member's samples"; public static final String FAMILY_EXPECTED_SIZE_DESCRIPTION = "Expected size of the family (number of members)"; - public static final String FAMILY_PHENOTYPES_DESCRIPTION = PHENOTYPES_DESCRIPTION + REGEX_SUPPORT; - public static final String FAMILY_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION + REGEX_SUPPORT; + public static final String FAMILY_PHENOTYPES_DESCRIPTION = PHENOTYPES_DESCRIPTION; + public static final String FAMILY_DISORDERS_DESCRIPTION = DISORDERS_DESCRIPTION; public static final String FAMILY_CREATION_DATE_DESCRIPTION = CREATION_DATE_DESCRIPTION; public static final String FAMILY_MODIFICATION_DATE_DESCRIPTION = MODIFICATION_DATE_DESCRIPTION; public static final String FAMILY_DELETED_DESCRIPTION = DELETED_DESCRIPTION; @@ -1480,7 +1480,7 @@ public class ParamConstants { public static final String FILES_ID_DESCRIPTION = "Comma separated list of file IDs" + UP_TO_100 + REGEX_SUPPORT; public static final String FILES_UUID_DESCRIPTION = "Comma separated list file UUIDs" + UP_TO_100; public static final String SAMPLES_DESCRIPTION = "Comma separated list sample IDs or UUIDs" + UP_TO_100; - public static final String SAMPLES_ID_DESCRIPTION = "Comma separated list sample IDs" + UP_TO_100; + public static final String SAMPLES_ID_DESCRIPTION = "Comma separated list sample IDs" + UP_TO_100 + REGEX_SUPPORT; public static final String SAMPLES_UUID_DESCRIPTION = "Comma separated list sample UUIDs" + UP_TO_100; public static final String INDIVIDUALS_DESCRIPTION = "Comma separated list of individual IDs, names or UUIDs" + UP_TO_100; public static final String INDIVIDUALS_ID_DESCRIPTION = "Comma separated list individual IDs" + UP_TO_100 + REGEX_SUPPORT; From cf6c1f136519b50629146f53bbe242f55c79bc90 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Wed, 30 Aug 2023 17:38:03 +0100 Subject: [PATCH 096/109] core: Do not validate empty string tokens. #TASK-4913 --- .../org/opencb/opencga/core/cellbase/CellBaseValidator.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java b/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java index 43da58f396a..d1738dedf02 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java @@ -194,7 +194,9 @@ private CellBaseConfiguration validate(boolean autoComplete) throws IOException } } } - if (getToken() != null) { + if (StringUtils.isEmpty(getToken())) { + cellBaseConfiguration.setToken(null); + } else { // Check it's supported if (!supportsToken(serverVersion)) { throw new IllegalArgumentException("Token not supported for cellbase " From b54ca18149aea527546f90261d0d0b96c05159e0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Thu, 31 Aug 2023 10:05:31 +0100 Subject: [PATCH 097/109] core: Improve exception message #TASK-4913 --- .../opencga/analysis/variant/manager/VariantStorageManager.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java index 806fbb6d818..cf5164f727a 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java @@ -1225,7 +1225,7 @@ private R secureTool(String toolId, boolean isOperation, ObjectMap params, S throw e; } catch (Exception e) { exception = e; - throw new StorageEngineException("Error executing operation " + toolId, e); + throw new StorageEngineException("Error executing operation '" + toolId + "' : " + e.getMessage(), e); } finally { if (result instanceof DataResult) { auditAttributes.append("dbTime", ((DataResult) result).getTime()); From ba9e611655319bd6452113578a438a636dfd2009 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Thu, 31 Aug 2023 11:15:12 +0100 Subject: [PATCH 098/109] core: Fix validation test #TASK-4913 --- .../analysis/variant/manager/VariantStorageManager.java | 8 +++++++- .../opencb/opencga/core/cellbase/CellBaseValidator.java | 5 +++-- .../opencga/core/cellbase/CellBaseValidatorTest.java | 8 ++++++++ 3 files changed, 18 insertions(+), 3 deletions(-) diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java index cf5164f727a..48b5cf87114 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java @@ -49,6 +49,7 @@ import org.opencb.opencga.catalog.managers.StudyManager; import org.opencb.opencga.core.api.ParamConstants; import org.opencb.opencga.core.cellbase.CellBaseValidator; +import org.opencb.opencga.core.common.ExceptionUtils; import org.opencb.opencga.core.common.UriUtils; import org.opencb.opencga.core.config.storage.CellBaseConfiguration; import org.opencb.opencga.core.config.storage.SampleIndexConfiguration; @@ -564,7 +565,10 @@ public OpenCGAResult setCellbaseConfiguration(String project, CellBaseConfi String annotationSaveId, String token) throws CatalogException, StorageEngineException { StopWatch stopwatch = StopWatch.createStarted(); - return secureOperationByProject("configureCellbase", project, new ObjectMap(), token, engine -> { + return secureOperationByProject("configureCellbase", project, new ObjectMap() + .append("cellbaseConfiguration", cellbaseConfiguration) + .append("annotate", annotate) + .append("annotationSaveId", annotationSaveId), token, engine -> { OpenCGAResult result = new OpenCGAResult<>(); result.setResultType(Job.class.getCanonicalName()); result.setResults(new ArrayList<>()); @@ -1237,6 +1241,8 @@ private R secureTool(String toolId, boolean isOperation, ObjectMap params, S if (exception != null) { auditAttributes.append("errorType", exception.getClass()); auditAttributes.append("errorMessage", exception.getMessage()); + auditAttributes.append("errorMessageFull", ExceptionUtils.prettyExceptionMessage(exception, false, true)); + auditAttributes.append("exceptionStackTrace", ExceptionUtils.prettyExceptionStackTrace(exception)); status = new AuditRecord.Status(AuditRecord.Status.Result.ERROR, new Error(-1, exception.getClass().getName(), exception.getMessage())); } else { diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java b/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java index d1738dedf02..467dabf7b75 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java @@ -194,7 +194,8 @@ private CellBaseConfiguration validate(boolean autoComplete) throws IOException } } } - if (StringUtils.isEmpty(getToken())) { + String token = getToken(); + if (StringUtils.isEmpty(token)) { cellBaseConfiguration.setToken(null); } else { // Check it's supported @@ -207,7 +208,7 @@ private CellBaseConfiguration validate(boolean autoComplete) throws IOException // Check it's an actual token DataAccessTokenManager tokenManager = new DataAccessTokenManager(); try { - tokenManager.decode(getToken()); + tokenManager.decode(token); } catch (JwtException e) { throw new IllegalArgumentException("Malformed token for cellbase " + "url: '" + getURL() + "'" diff --git a/opencga-core/src/test/java/org/opencb/opencga/core/cellbase/CellBaseValidatorTest.java b/opencga-core/src/test/java/org/opencb/opencga/core/cellbase/CellBaseValidatorTest.java index 38d91dd0fc8..36026700237 100644 --- a/opencga-core/src/test/java/org/opencb/opencga/core/cellbase/CellBaseValidatorTest.java +++ b/opencga-core/src/test/java/org/opencb/opencga/core/cellbase/CellBaseValidatorTest.java @@ -85,10 +85,18 @@ public void testToken() throws IOException { public void testTokenNotSupported() throws IOException { String token = System.getenv("CELLBASE_HGMD_TOKEN"); Assume.assumeTrue(StringUtils.isNotEmpty(token)); + thrown.expectMessage("Token not supported"); CellBaseConfiguration validated = CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.1", null, token), "hsapiens", "grch38", true); Assert.assertNotNull(validated.getToken()); } + @Test + public void testTokenEmpty() throws IOException { + String token = ""; + CellBaseConfiguration validated = CellBaseValidator.validate(new CellBaseConfiguration(ParamConstants.CELLBASE_URL, "v5.1", null, token), "hsapiens", "grch38", true); + Assert.assertNull(validated.getToken()); + } + @Test public void testMalformedToken() throws IOException { thrown.expectMessage("Malformed token for cellbase"); From 7e29141346bf4153eff9d13c8f4dbe8de947f237 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Mon, 4 Sep 2023 12:31:29 +0200 Subject: [PATCH 099/109] Prepare merge --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-deps-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp2.6/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 2 +- 21 files changed, 21 insertions(+), 21 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 260955d38c6..adcb53e2d0e 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 4d18a6476ca..b787e5d11d2 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index a0ea06ca14c..fac7d8e548a 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 191a5319867..22a563296b0 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index a9630add90e..de52a8ef4e1 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 508d50cede8..e2d8fc127e4 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index d45f901844c..2d6fd5a8da6 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 0d66c9f3a74..65cebaebdda 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 9d41b4d028d..cafb6d1c2ac 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 89d8c6c9d7e..aa79ec720fd 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 3b2f329ccb0..b97d0472984 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -25,7 +25,7 @@ org.opencb.opencga opencga-storage - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index bd7a7c7baa4..97db69b63b9 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml index f64c1bc25ba..1c27bd10350 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml index a5852716f29..f1f99b70468 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml index cbbfa9c0e83..03561e6c93d 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml index 3dc7eedf5dc..c0e60a63db5 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml @@ -50,7 +50,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 202510b2e48..1ea5e5a91d1 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -28,7 +28,7 @@ org.opencb.opencga opencga-storage - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index bbe30f1aa3b..c9a6b5604a3 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index ab93e1a8071..49b680170d0 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 8f13ebd49ab..caa613c03e2 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 2.8.3 + 2.11.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index a91ad02aa54..6cdcc114b77 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.8.3 + 2.11.0-SNAPSHOT pom OpenCGA OenCGA projects implements a big data platform for genomic data analysis From 92558f56ec8f5c243385da948796d374a4875517 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?= Date: Thu, 7 Sep 2023 15:26:26 +0200 Subject: [PATCH 100/109] core: rename token to apiKey in some functions, #TASK-4898, #TASK-4641 --- .../opencb/opencga/core/cellbase/CellBaseValidator.java | 8 ++++---- .../annotators/AbstractCellBaseVariantAnnotator.java | 4 ++-- .../annotators/CellBaseRestVariantAnnotator.java | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java b/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java index 61f718dd785..edf5e3e50bc 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/cellbase/CellBaseValidator.java @@ -198,7 +198,7 @@ private CellBaseConfiguration validate(boolean autoComplete) throws IOException cellBaseConfiguration.setApiKey(null); } else { // Check it's supported - if (!supportsToken(serverVersion)) { + if (!supportsApiKey(serverVersion)) { throw new IllegalArgumentException("API key not supported for cellbase " + "url: '" + getURL() + "'" + ", version: '" + inputVersion + "'"); @@ -270,8 +270,8 @@ public static boolean supportsDataReleaseActiveByDefaultIn(String serverVersion) return VersionUtils.isMinVersion("5.5.0", serverVersion, true); } - public static boolean supportsToken(String serverVersion) { - // Tokens support starts at version 5.4.0 + public static boolean supportsApiKey(String serverVersion) { + // API keys support starts at version 5.4.0 return VersionUtils.isMinVersion("5.4.0", serverVersion); } @@ -325,7 +325,7 @@ public String toString() { + "species '" + getSpecies() + "', " + "assembly '" + getAssembly() + "', " + "dataRelease '" + getDataRelease() + "', " - + "token '" + getApiKey() + "'"; + + "apiKey '" + getApiKey() + "'"; } } diff --git a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/AbstractCellBaseVariantAnnotator.java b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/AbstractCellBaseVariantAnnotator.java index fc743b13a76..da8d44b05b5 100644 --- a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/AbstractCellBaseVariantAnnotator.java +++ b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/AbstractCellBaseVariantAnnotator.java @@ -56,7 +56,7 @@ public abstract class AbstractCellBaseVariantAnnotator extends VariantAnnotator protected final String assembly; protected final String cellbaseVersion; protected final String cellbaseDataRelease; - protected final String cellbaseToken; + protected final String cellbaseApiKey; protected final QueryOptions queryOptions; protected final boolean supportImpreciseVariants; protected final boolean supportStarAlternate; @@ -72,7 +72,7 @@ public AbstractCellBaseVariantAnnotator(StorageConfiguration storageConfiguratio assembly = projectMetadata.getAssembly(); cellbaseVersion = storageConfiguration.getCellbase().getVersion(); cellbaseDataRelease = storageConfiguration.getCellbase().getDataRelease(); - cellbaseToken = storageConfiguration.getCellbase().getApiKey(); + cellbaseApiKey = storageConfiguration.getCellbase().getApiKey(); queryOptions = new QueryOptions(); if (StringUtils.isNotEmpty(params.getString(VariantStorageOptions.ANNOTATOR_CELLBASE_INCLUDE.key()))) { diff --git a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/CellBaseRestVariantAnnotator.java b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/CellBaseRestVariantAnnotator.java index 85ee3b0810c..a589a21e1a4 100644 --- a/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/CellBaseRestVariantAnnotator.java +++ b/opencga-storage/opencga-storage-core/src/main/java/org/opencb/opencga/storage/core/variant/annotation/annotators/CellBaseRestVariantAnnotator.java @@ -67,7 +67,7 @@ public CellBaseRestVariantAnnotator(StorageConfiguration storageConfiguration, P VariantStorageOptions.ANNOTATION_TIMEOUT.defaultValue()); clientConfiguration.getRest().setTimeout(timeoutMillis); - cellBaseClient = new CellBaseClient(species, assembly, cellbaseDataRelease, cellbaseToken, clientConfiguration); + cellBaseClient = new CellBaseClient(species, assembly, cellbaseDataRelease, cellbaseApiKey, clientConfiguration); cellBaseUtils = new CellBaseUtils(cellBaseClient); logger.info("Annotating with Cellbase REST. {}", cellBaseUtils); From 9b9ee1c44a9c4ce6e34a3f600d1e4ebc62080ffb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?= Date: Fri, 8 Sep 2023 08:29:43 +0200 Subject: [PATCH 101/109] analysis: use the project API key before using the storage API key, #TASK-4898, #TASK-4641 --- .../analysis/variant/manager/VariantStorageManager.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java index e62528b6d28..22b337e9621 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/variant/manager/VariantStorageManager.java @@ -1021,7 +1021,8 @@ private void setCellbaseConfiguration(VariantStorageEngine engine, String projec .get(project, new QueryOptions(INCLUDE, ProjectDBAdaptor.QueryParams.CELLBASE.key()), token) .first().getCellbase(); if (cellbase != null) { - if (StringUtils.isEmpty(cellbase.getApiKey()) || storageConfiguration.getCellbase() != null) { + // To ensure that we use the project API key before using the storage API key + if (StringUtils.isEmpty(cellbase.getApiKey()) && storageConfiguration.getCellbase() != null) { cellbase.setApiKey(storageConfiguration.getCellbase().getApiKey()); } engine.getConfiguration().setCellbase(cellbase); From 9ac3dfcce928664c921cd93dbbb2662d86fb6593 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= Date: Fri, 8 Sep 2023 11:07:23 +0100 Subject: [PATCH 102/109] storage: Do fail when export-snapshot fails #TASK-4372 --- .../opencga/storage/hadoop/app/HBaseMain.java | 53 +++++++++++-------- 1 file changed, 32 insertions(+), 21 deletions(-) diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/app/HBaseMain.java b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/app/HBaseMain.java index f713fbc2e9e..4daa7789327 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/app/HBaseMain.java +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/src/main/java/org/opencb/opencga/storage/hadoop/app/HBaseMain.java @@ -214,23 +214,23 @@ public void run(String[] args) throws Exception { + "[--onExistingTables [fail|skip|drop] ]"); System.out.println(" Clone all snapshots into tables matching the regex. " + "Generated tables can have a table prefix change."); -// System.out.println(" " + EXPORT_SNAPSHOTS + " \n" -// + " --dryRun Dry run.\n" -// + " --snapshot Snapshot to restore.\n" -// + " --copyTo Remote destination hdfs://\n" -// + " --copyFrom Input folder hdfs:// (default hbase.rootdir)\n" -// + " --target Target name for the snapshot.\n" -//// + " --no-checksum-verify Do not verify checksum, use name+length only.\n" -//// + " --no-target-verify Do not verify the integrity of the exported snapshot.\n" -// + " --overwrite Rewrite the snapshot manifest if already exists.\n" -//// + " --chuser Change the owner of the files to the specified one.\n" -//// + " --chgroup Change the group of the files to the specified one.\n" -//// + " --chmod Change the permission of the files to the specified one.\n" -//// + " --bandwidth Limit bandwidth to this value in MB/second.\n" -// + " --mappers Number of mappers to use during the copy (mapreduce.job.maps).\n" -// + " -Dkey=value Other key-value fields"); -// System.out.println(" Clone all snapshots into tables matching the regex. " -// + "Generated tables can have a table prefix change."); + System.out.println(" " + EXPORT_SNAPSHOTS + " \n" + + " --dryRun Dry run.\n" + + " --snapshot Snapshot to restore.\n" + + " --copy-to Remote destination hdfs://\n" + + " --copy-to-local Flag to indicate that must copy to local hbase.rootdir (for imports)\n" + + " --copy-from Input folder hdfs:// (default hbase.rootdir)\n" + + " --target Target name for the snapshot.\n" +// + " --no-checksum-verify Do not verify checksum, use name+length only.\n" +// + " --no-target-verify Do not verify the integrity of the exported snapshot.\n" + + " --overwrite Rewrite the snapshot manifest if already exists.\n" +// + " --chuser Change the owner of the files to the specified one.\n" +// + " --chgroup Change the group of the files to the specified one.\n" +// + " --chmod Change the permission of the files to the specified one.\n" +// + " --bandwidth Limit bandwidth to this value in MB/second.\n" + + " --mappers Number of mappers to use during the copy (mapreduce.job.maps).\n" + + " -Dkey=value Other key-value fields"); + System.out.println(" Export a given snapshot an external location."); System.out.println(" " + EXEC + "[hadoop|yarn|hbase|hdfs]"); System.out.println(" Execute a MR job on the hadoop cluster. Use \"exec yarn jar ....\""); System.out.println(" " + DISABLE_TABLE + " [--dryRun]"); @@ -258,7 +258,10 @@ private void exec(String tool, List args) throws Exception { engine.setConfiguration(storageConfiguration, HadoopVariantStorageEngine.STORAGE_ENGINE_ID, ""); MRExecutor mrExecutor = engine.getMRExecutor(); - mrExecutor.run(tool, args.toArray(new String[0])); + int exitError = mrExecutor.run(tool, args.toArray(new String[0])); + if (exitError != 0) { + throw new Exception("Exec failed with exit number '" + exitError + "'"); + } } private void exportSnapshot(String storageConfigurationPath, String snapshot, String copyTo, boolean copyToLocal, @@ -280,12 +283,17 @@ private void exportSnapshot(String storageConfigurationPath, String snapshot, St } args.add("--snapshot"); args.add(snapshot); + + args.add("--copy-to"); if (StringUtils.isNotEmpty(copyTo)) { - args.add("--copy-to"); args.add(copyTo); + if (copyToLocal) { + throw new Exception("Incompatible arguments `--copy-to` and `--copy-to-local`. Use only one of them"); + } } else if (copyToLocal) { - args.add("--copy-to"); args.add(hBaseManager.getConf().get(HConstants.HBASE_DIR)); + } else { + throw new Exception("Missing copy destination. Add either `--copy-to` or `--copy-to-local`"); } if (StringUtils.isNotEmpty(copyFrom)) { args.add("--copy-from"); @@ -310,7 +318,10 @@ private void exportSnapshot(String storageConfigurationPath, String snapshot, St engine.setConfiguration(storageConfiguration, HadoopVariantStorageEngine.STORAGE_ENGINE_ID, ""); MRExecutor mrExecutor = engine.getMRExecutor(); - mrExecutor.run("hbase", args.toArray(new String[0])); + int exitError = mrExecutor.run("hbase", args.toArray(new String[0])); + if (exitError != 0) { + throw new Exception("ExportSnapshot failed with exit number '" + exitError + "'"); + } } } From d65e9262985c223d49cf0edbdaf5cf2ac4331171 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Tue, 12 Sep 2023 10:30:37 +0200 Subject: [PATCH 103/109] CodeGen: generated CLI and Clients --- .../opencga/app/cli/main/OpenCgaCompleter.java | 2 +- .../app/cli/main/OpencgaCliOptionsParser.java | 2 +- opencga-client/src/main/R/R/Admin-methods.R | 2 +- .../src/main/R/R/Alignment-methods.R | 2 +- opencga-client/src/main/R/R/AllGenerics.R | 18 +++++++++--------- opencga-client/src/main/R/R/Clinical-methods.R | 4 ++-- opencga-client/src/main/R/R/Cohort-methods.R | 4 ++-- opencga-client/src/main/R/R/Family-methods.R | 4 ++-- opencga-client/src/main/R/R/File-methods.R | 4 ++-- opencga-client/src/main/R/R/GA4GH-methods.R | 4 ++-- .../src/main/R/R/Individual-methods.R | 4 ++-- opencga-client/src/main/R/R/Job-methods.R | 4 ++-- opencga-client/src/main/R/R/Meta-methods.R | 2 +- .../src/main/R/R/Operation-methods.R | 2 +- opencga-client/src/main/R/R/Panel-methods.R | 2 +- opencga-client/src/main/R/R/Project-methods.R | 2 +- opencga-client/src/main/R/R/Sample-methods.R | 4 ++-- opencga-client/src/main/R/R/Study-methods.R | 2 +- opencga-client/src/main/R/R/User-methods.R | 4 ++-- opencga-client/src/main/R/R/Variant-methods.R | 2 +- .../client/rest/clients/AdminClient.java | 2 +- .../client/rest/clients/AlignmentClient.java | 2 +- .../rest/clients/ClinicalAnalysisClient.java | 2 +- .../client/rest/clients/CohortClient.java | 2 +- .../rest/clients/DiseasePanelClient.java | 2 +- .../client/rest/clients/FamilyClient.java | 2 +- .../client/rest/clients/FileClient.java | 2 +- .../client/rest/clients/GA4GHClient.java | 2 +- .../client/rest/clients/IndividualClient.java | 2 +- .../opencga/client/rest/clients/JobClient.java | 2 +- .../client/rest/clients/MetaClient.java | 2 +- .../client/rest/clients/ProjectClient.java | 2 +- .../client/rest/clients/SampleClient.java | 2 +- .../client/rest/clients/StudyClient.java | 2 +- .../client/rest/clients/UserClient.java | 2 +- .../client/rest/clients/VariantClient.java | 2 +- .../rest/clients/VariantOperationClient.java | 2 +- opencga-client/src/main/javascript/Admin.js | 2 +- .../src/main/javascript/Alignment.js | 2 +- .../src/main/javascript/ClinicalAnalysis.js | 2 +- opencga-client/src/main/javascript/Cohort.js | 2 +- .../src/main/javascript/DiseasePanel.js | 2 +- opencga-client/src/main/javascript/Family.js | 2 +- opencga-client/src/main/javascript/File.js | 2 +- opencga-client/src/main/javascript/GA4GH.js | 2 +- .../src/main/javascript/Individual.js | 2 +- opencga-client/src/main/javascript/Job.js | 2 +- opencga-client/src/main/javascript/Meta.js | 2 +- opencga-client/src/main/javascript/Project.js | 2 +- opencga-client/src/main/javascript/Sample.js | 2 +- opencga-client/src/main/javascript/Study.js | 2 +- opencga-client/src/main/javascript/User.js | 2 +- opencga-client/src/main/javascript/Variant.js | 2 +- .../src/main/javascript/VariantOperation.js | 2 +- .../pyopencga/rest_clients/admin_client.py | 2 +- .../pyopencga/rest_clients/alignment_client.py | 2 +- .../rest_clients/clinical_analysis_client.py | 2 +- .../pyopencga/rest_clients/cohort_client.py | 2 +- .../rest_clients/disease_panel_client.py | 2 +- .../pyopencga/rest_clients/family_client.py | 2 +- .../pyopencga/rest_clients/file_client.py | 2 +- .../pyopencga/rest_clients/ga4gh_client.py | 2 +- .../rest_clients/individual_client.py | 2 +- .../pyopencga/rest_clients/job_client.py | 2 +- .../pyopencga/rest_clients/meta_client.py | 2 +- .../pyopencga/rest_clients/project_client.py | 2 +- .../pyopencga/rest_clients/sample_client.py | 2 +- .../pyopencga/rest_clients/study_client.py | 2 +- .../pyopencga/rest_clients/user_client.py | 2 +- .../pyopencga/rest_clients/variant_client.py | 2 +- .../rest_clients/variant_operation_client.py | 2 +- 71 files changed, 88 insertions(+), 88 deletions(-) diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java index b023618b21f..ee9f603f739 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023-09-08 OpenCB +* Copyright 2015-2023-09-12 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java index 93ae1e2ed26..832d5638d49 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java @@ -1,5 +1,5 @@ /* -* Copyright 2015-2023-09-08 OpenCB +* Copyright 2015-2023-09-12 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/opencga-client/src/main/R/R/Admin-methods.R b/opencga-client/src/main/R/R/Admin-methods.R index 52e55fc3918..f36ae979df6 100644 --- a/opencga-client/src/main/R/R/Admin-methods.R +++ b/opencga-client/src/main/R/R/Admin-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-08 +# Autogenerated on: 2023-09-12 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Alignment-methods.R b/opencga-client/src/main/R/R/Alignment-methods.R index 66dcf64a9a4..7f1a6a2d745 100644 --- a/opencga-client/src/main/R/R/Alignment-methods.R +++ b/opencga-client/src/main/R/R/Alignment-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-08 +# Autogenerated on: 2023-09-12 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/AllGenerics.R b/opencga-client/src/main/R/R/AllGenerics.R index 2b49e7247d0..5756f579584 100644 --- a/opencga-client/src/main/R/R/AllGenerics.R +++ b/opencga-client/src/main/R/R/AllGenerics.R @@ -1,6 +1,6 @@ # ############################################################################## ## UserClient -setGeneric("userClient", function(OpencgaR, users, user, filterId, endpointName, params=NULL, ...) +setGeneric("userClient", function(OpencgaR, filterId, user, users, endpointName, params=NULL, ...) standardGeneric("userClient")) # ############################################################################## @@ -15,32 +15,32 @@ setGeneric("studyClient", function(OpencgaR, study, group, variableSet, studies, # ############################################################################## ## FileClient -setGeneric("fileClient", function(OpencgaR, folder, annotationSet, file, members, files, endpointName, params=NULL, ...) +setGeneric("fileClient", function(OpencgaR, file, files, folder, members, annotationSet, endpointName, params=NULL, ...) standardGeneric("fileClient")) # ############################################################################## ## JobClient -setGeneric("jobClient", function(OpencgaR, members, jobs, job, endpointName, params=NULL, ...) +setGeneric("jobClient", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...) standardGeneric("jobClient")) # ############################################################################## ## SampleClient -setGeneric("sampleClient", function(OpencgaR, samples, members, sample, annotationSet, endpointName, params=NULL, ...) +setGeneric("sampleClient", function(OpencgaR, sample, members, annotationSet, samples, endpointName, params=NULL, ...) standardGeneric("sampleClient")) # ############################################################################## ## IndividualClient -setGeneric("individualClient", function(OpencgaR, individuals, members, individual, annotationSet, endpointName, params=NULL, ...) +setGeneric("individualClient", function(OpencgaR, members, annotationSet, individuals, individual, endpointName, params=NULL, ...) standardGeneric("individualClient")) # ############################################################################## ## FamilyClient -setGeneric("familyClient", function(OpencgaR, family, members, families, annotationSet, endpointName, params=NULL, ...) +setGeneric("familyClient", function(OpencgaR, families, members, annotationSet, family, endpointName, params=NULL, ...) standardGeneric("familyClient")) # ############################################################################## ## CohortClient -setGeneric("cohortClient", function(OpencgaR, annotationSet, members, cohort, cohorts, endpointName, params=NULL, ...) +setGeneric("cohortClient", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) standardGeneric("cohortClient")) # ############################################################################## @@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## ClinicalClient -setGeneric("clinicalClient", function(OpencgaR, clinicalAnalyses, interpretation, clinicalAnalysis, interpretations, members, endpointName, params=NULL, ...) +setGeneric("clinicalClient", function(OpencgaR, interpretation, interpretations, clinicalAnalysis, clinicalAnalyses, members, endpointName, params=NULL, ...) standardGeneric("clinicalClient")) # ############################################################################## @@ -75,7 +75,7 @@ setGeneric("metaClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## GA4GHClient -setGeneric("ga4ghClient", function(OpencgaR, study, file, endpointName, params=NULL, ...) +setGeneric("ga4ghClient", function(OpencgaR, file, study, endpointName, params=NULL, ...) standardGeneric("ga4ghClient")) # ############################################################################## diff --git a/opencga-client/src/main/R/R/Clinical-methods.R b/opencga-client/src/main/R/R/Clinical-methods.R index 36200235c2a..5d84fa14614 100644 --- a/opencga-client/src/main/R/R/Clinical-methods.R +++ b/opencga-client/src/main/R/R/Clinical-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-08 +# Autogenerated on: 2023-09-12 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -58,7 +58,7 @@ #' [*]: Required parameter #' @export -setMethod("clinicalClient", "OpencgaR", function(OpencgaR, clinicalAnalyses, interpretation, clinicalAnalysis, interpretations, members, endpointName, params=NULL, ...) { +setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretation, interpretations, clinicalAnalysis, clinicalAnalyses, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R index 3ae1d7734b5..d192d6feec1 100644 --- a/opencga-client/src/main/R/R/Cohort-methods.R +++ b/opencga-client/src/main/R/R/Cohort-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-08 +# Autogenerated on: 2023-09-12 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("cohortClient", "OpencgaR", function(OpencgaR, annotationSet, members, cohort, cohorts, endpointName, params=NULL, ...) { +setMethod("cohortClient", "OpencgaR", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Family-methods.R b/opencga-client/src/main/R/R/Family-methods.R index ffeb618a259..c582b23a93a 100644 --- a/opencga-client/src/main/R/R/Family-methods.R +++ b/opencga-client/src/main/R/R/Family-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-08 +# Autogenerated on: 2023-09-12 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("familyClient", "OpencgaR", function(OpencgaR, family, members, families, annotationSet, endpointName, params=NULL, ...) { +setMethod("familyClient", "OpencgaR", function(OpencgaR, families, members, annotationSet, family, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/families/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/File-methods.R b/opencga-client/src/main/R/R/File-methods.R index 5db25da7799..f3eeac80df2 100644 --- a/opencga-client/src/main/R/R/File-methods.R +++ b/opencga-client/src/main/R/R/File-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-08 +# Autogenerated on: 2023-09-12 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -54,7 +54,7 @@ #' [*]: Required parameter #' @export -setMethod("fileClient", "OpencgaR", function(OpencgaR, folder, annotationSet, file, members, files, endpointName, params=NULL, ...) { +setMethod("fileClient", "OpencgaR", function(OpencgaR, file, files, folder, members, annotationSet, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/files/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/GA4GH-methods.R b/opencga-client/src/main/R/R/GA4GH-methods.R index 8aae23ad4a6..639683e171c 100644 --- a/opencga-client/src/main/R/R/GA4GH-methods.R +++ b/opencga-client/src/main/R/R/GA4GH-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-08 +# Autogenerated on: 2023-09-12 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -31,7 +31,7 @@ #' [*]: Required parameter #' @export -setMethod("ga4ghClient", "OpencgaR", function(OpencgaR, study, file, endpointName, params=NULL, ...) { +setMethod("ga4ghClient", "OpencgaR", function(OpencgaR, file, study, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/ga4gh/reads/search: diff --git a/opencga-client/src/main/R/R/Individual-methods.R b/opencga-client/src/main/R/R/Individual-methods.R index 35b01f1ce71..1839f2cb8c9 100644 --- a/opencga-client/src/main/R/R/Individual-methods.R +++ b/opencga-client/src/main/R/R/Individual-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-08 +# Autogenerated on: 2023-09-12 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("individualClient", "OpencgaR", function(OpencgaR, individuals, members, individual, annotationSet, endpointName, params=NULL, ...) { +setMethod("individualClient", "OpencgaR", function(OpencgaR, members, annotationSet, individuals, individual, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/individuals/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Job-methods.R b/opencga-client/src/main/R/R/Job-methods.R index d61eb46c702..ed70e8df6cf 100644 --- a/opencga-client/src/main/R/R/Job-methods.R +++ b/opencga-client/src/main/R/R/Job-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-08 +# Autogenerated on: 2023-09-12 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -40,7 +40,7 @@ #' [*]: Required parameter #' @export -setMethod("jobClient", "OpencgaR", function(OpencgaR, members, jobs, job, endpointName, params=NULL, ...) { +setMethod("jobClient", "OpencgaR", function(OpencgaR, members, job, jobs, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/jobs/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Meta-methods.R b/opencga-client/src/main/R/R/Meta-methods.R index 100a6e11e6f..c278a0c47e4 100644 --- a/opencga-client/src/main/R/R/Meta-methods.R +++ b/opencga-client/src/main/R/R/Meta-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-08 +# Autogenerated on: 2023-09-12 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Operation-methods.R b/opencga-client/src/main/R/R/Operation-methods.R index 73e41e1eefe..11621e2cf87 100644 --- a/opencga-client/src/main/R/R/Operation-methods.R +++ b/opencga-client/src/main/R/R/Operation-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-08 +# Autogenerated on: 2023-09-12 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Panel-methods.R b/opencga-client/src/main/R/R/Panel-methods.R index bf61ce54f10..20fb425cc31 100644 --- a/opencga-client/src/main/R/R/Panel-methods.R +++ b/opencga-client/src/main/R/R/Panel-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-08 +# Autogenerated on: 2023-09-12 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Project-methods.R b/opencga-client/src/main/R/R/Project-methods.R index 3911d6f5f9a..80d88c4cc79 100644 --- a/opencga-client/src/main/R/R/Project-methods.R +++ b/opencga-client/src/main/R/R/Project-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-08 +# Autogenerated on: 2023-09-12 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Sample-methods.R b/opencga-client/src/main/R/R/Sample-methods.R index 44d4e5e58bb..32e64a3ecc9 100644 --- a/opencga-client/src/main/R/R/Sample-methods.R +++ b/opencga-client/src/main/R/R/Sample-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-08 +# Autogenerated on: 2023-09-12 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("sampleClient", "OpencgaR", function(OpencgaR, samples, members, sample, annotationSet, endpointName, params=NULL, ...) { +setMethod("sampleClient", "OpencgaR", function(OpencgaR, sample, members, annotationSet, samples, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/samples/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Study-methods.R b/opencga-client/src/main/R/R/Study-methods.R index ab51f6a4a8d..a9c9a3c90f8 100644 --- a/opencga-client/src/main/R/R/Study-methods.R +++ b/opencga-client/src/main/R/R/Study-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-08 +# Autogenerated on: 2023-09-12 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/User-methods.R b/opencga-client/src/main/R/R/User-methods.R index 671c70ca6c9..2a1d1bc3e82 100644 --- a/opencga-client/src/main/R/R/User-methods.R +++ b/opencga-client/src/main/R/R/User-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-08 +# Autogenerated on: 2023-09-12 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("userClient", "OpencgaR", function(OpencgaR, users, user, filterId, endpointName, params=NULL, ...) { +setMethod("userClient", "OpencgaR", function(OpencgaR, filterId, user, users, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/users/login: diff --git a/opencga-client/src/main/R/R/Variant-methods.R b/opencga-client/src/main/R/R/Variant-methods.R index 911cd8ecc94..ad760abcd16 100644 --- a/opencga-client/src/main/R/R/Variant-methods.R +++ b/opencga-client/src/main/R/R/Variant-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2023-09-08 +# Autogenerated on: 2023-09-12 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java index b4b8cc001d6..6aad0bc7842 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-08 +* Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java index ae7aef83174..16c679f642f 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java @@ -40,7 +40,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-08 +* Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java index 912ef505958..94ab79f677d 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java @@ -51,7 +51,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-08 +* Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java index 88cc7b62b23..2320ca7bbcd 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java @@ -37,7 +37,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-08 +* Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java index 61f2af635da..ad9ef470eaa 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java @@ -35,7 +35,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-08 +* Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java index 6280a7026e0..94b0e7cf66d 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-08 +* Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java index ce6df1ebb2e..94eeead7197 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java @@ -43,7 +43,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-08 +* Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java index 28170cb2746..48b4524ea7f 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java @@ -27,7 +27,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-08 +* Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java index eb24455c52a..b89c47024df 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-08 +* Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java index 68934888520..7945a8d65cc 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java @@ -37,7 +37,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-08 +* Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java index b68b929186c..794c6ad3394 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java @@ -28,7 +28,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-08 +* Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java index 395b4593856..317a4af226c 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java @@ -32,7 +32,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-08 +* Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java index f2874078762..5cbb8f10fd4 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-08 +* Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java index 6216f78b94b..8f018861260 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java @@ -45,7 +45,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-08 +* Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java index 93c49bdf998..adb4ce85938 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-08 +* Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java index c96321b199a..4801650a0f9 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java @@ -62,7 +62,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-08 +* Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java index 4b870042648..c1ffc952c9d 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java @@ -50,7 +50,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2023-09-08 +* Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Admin.js b/opencga-client/src/main/javascript/Admin.js index 5edf0a466c6..2466edfccfd 100644 --- a/opencga-client/src/main/javascript/Admin.js +++ b/opencga-client/src/main/javascript/Admin.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-08 + * Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Alignment.js b/opencga-client/src/main/javascript/Alignment.js index 874adaf6b67..446219c5a59 100644 --- a/opencga-client/src/main/javascript/Alignment.js +++ b/opencga-client/src/main/javascript/Alignment.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-08 + * Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/ClinicalAnalysis.js b/opencga-client/src/main/javascript/ClinicalAnalysis.js index 7b04cf20cdd..221fa4a68da 100644 --- a/opencga-client/src/main/javascript/ClinicalAnalysis.js +++ b/opencga-client/src/main/javascript/ClinicalAnalysis.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-08 + * Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Cohort.js b/opencga-client/src/main/javascript/Cohort.js index 139868db04d..9d070dc8ec8 100644 --- a/opencga-client/src/main/javascript/Cohort.js +++ b/opencga-client/src/main/javascript/Cohort.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-08 + * Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/DiseasePanel.js b/opencga-client/src/main/javascript/DiseasePanel.js index 2f8e596a9a9..1d97f0d3b6f 100644 --- a/opencga-client/src/main/javascript/DiseasePanel.js +++ b/opencga-client/src/main/javascript/DiseasePanel.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-08 + * Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Family.js b/opencga-client/src/main/javascript/Family.js index ffd436567e0..5b11ceacd3a 100644 --- a/opencga-client/src/main/javascript/Family.js +++ b/opencga-client/src/main/javascript/Family.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-08 + * Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/File.js b/opencga-client/src/main/javascript/File.js index a2455a0953f..27d76b733e7 100644 --- a/opencga-client/src/main/javascript/File.js +++ b/opencga-client/src/main/javascript/File.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-08 + * Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/GA4GH.js b/opencga-client/src/main/javascript/GA4GH.js index f5e18645184..2e3f968ab05 100644 --- a/opencga-client/src/main/javascript/GA4GH.js +++ b/opencga-client/src/main/javascript/GA4GH.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-08 + * Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Individual.js b/opencga-client/src/main/javascript/Individual.js index da0324012b5..160bb589c50 100644 --- a/opencga-client/src/main/javascript/Individual.js +++ b/opencga-client/src/main/javascript/Individual.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-08 + * Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Job.js b/opencga-client/src/main/javascript/Job.js index 1125c50f9f1..52f5cdde599 100644 --- a/opencga-client/src/main/javascript/Job.js +++ b/opencga-client/src/main/javascript/Job.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-08 + * Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Meta.js b/opencga-client/src/main/javascript/Meta.js index ca2c12b459b..0207e95847a 100644 --- a/opencga-client/src/main/javascript/Meta.js +++ b/opencga-client/src/main/javascript/Meta.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-08 + * Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Project.js b/opencga-client/src/main/javascript/Project.js index 9ed80c76552..f43c7394d71 100644 --- a/opencga-client/src/main/javascript/Project.js +++ b/opencga-client/src/main/javascript/Project.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-08 + * Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Sample.js b/opencga-client/src/main/javascript/Sample.js index ebe4b047ade..edefccf3e5a 100644 --- a/opencga-client/src/main/javascript/Sample.js +++ b/opencga-client/src/main/javascript/Sample.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-08 + * Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Study.js b/opencga-client/src/main/javascript/Study.js index 09159e5bc29..d153ba9d316 100644 --- a/opencga-client/src/main/javascript/Study.js +++ b/opencga-client/src/main/javascript/Study.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-08 + * Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/User.js b/opencga-client/src/main/javascript/User.js index bd11746e1de..d8c60b8d409 100644 --- a/opencga-client/src/main/javascript/User.js +++ b/opencga-client/src/main/javascript/User.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-08 + * Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Variant.js b/opencga-client/src/main/javascript/Variant.js index 34884a86bb7..35617fde07f 100644 --- a/opencga-client/src/main/javascript/Variant.js +++ b/opencga-client/src/main/javascript/Variant.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-08 + * Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/VariantOperation.js b/opencga-client/src/main/javascript/VariantOperation.js index 2ce54e16534..daa6917728a 100644 --- a/opencga-client/src/main/javascript/VariantOperation.js +++ b/opencga-client/src/main/javascript/VariantOperation.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2023-09-08 + * Autogenerated on: 2023-09-12 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py index 53fdc052390..28598b602eb 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-08 + Autogenerated on: 2023-09-12 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py index 091948e5f53..d19895d21ba 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-08 + Autogenerated on: 2023-09-12 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py index 83ab4dbb7da..cf8de0798c5 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-08 + Autogenerated on: 2023-09-12 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py index 445f4a66826..f7d6ad80542 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-08 + Autogenerated on: 2023-09-12 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py index fdf80361f55..6d47ea09d3c 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-08 + Autogenerated on: 2023-09-12 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py index 6642396fb41..65e3a070dce 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-08 + Autogenerated on: 2023-09-12 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py index 45719c4b213..c6c028d3b3a 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-08 + Autogenerated on: 2023-09-12 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py index a7ec7e99b6c..48e5b17de75 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-08 + Autogenerated on: 2023-09-12 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py index 044a326dd67..07dd3d04b0d 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-08 + Autogenerated on: 2023-09-12 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py index eeda7834cd9..d692f8e099c 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-08 + Autogenerated on: 2023-09-12 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py index bee9670a694..d43227b33f8 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-08 + Autogenerated on: 2023-09-12 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py index c3b4c0a9e38..bd29b4b1013 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-08 + Autogenerated on: 2023-09-12 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py index 7cf520ad6c0..fcb5c944884 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-08 + Autogenerated on: 2023-09-12 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py index 09a0d3d5e96..40cc9a63c08 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-08 + Autogenerated on: 2023-09-12 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py index c05e00b0e30..3f2ed4eae3e 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-08 + Autogenerated on: 2023-09-12 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py index 7a2081d3bbb..80e1746470a 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-08 + Autogenerated on: 2023-09-12 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py index 775c3130a2b..4297fbf08ae 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2023-09-08 + Autogenerated on: 2023-09-12 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. From dc9cf1b0079b2999587c7053647fee2751b408f2 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 20 Sep 2023 13:28:26 +0200 Subject: [PATCH 104/109] Prepare release 2.11.0 --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-deps-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp2.6/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 21 files changed, 27 insertions(+), 27 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index adcb53e2d0e..75aeacc0f1b 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.11.0-SNAPSHOT + 2.11.0 ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index aaa0506b93b..1c574488bb2 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.11.0-SNAPSHOT + 2.11.0 ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index fac7d8e548a..6fdf8029ab9 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 2.11.0-SNAPSHOT + 2.11.0 ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index 22a563296b0..b7e5033cc84 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.11.0-SNAPSHOT + 2.11.0 ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index de52a8ef4e1..1e1394cc92a 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 2.11.0-SNAPSHOT + 2.11.0 ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index b8e72cfb0c1..2d131098bbd 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.11.0-SNAPSHOT + 2.11.0 ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 2d6fd5a8da6..0ea519d70d4 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 2.11.0-SNAPSHOT + 2.11.0 ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 65cebaebdda..2d636201f53 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.11.0-SNAPSHOT + 2.11.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index cafb6d1c2ac..5a2f15e6fac 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.11.0-SNAPSHOT + 2.11.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index aa79ec720fd..00921cbe8e6 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 2.11.0-SNAPSHOT + 2.11.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index b97d0472984..0875ba3e255 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -25,7 +25,7 @@ org.opencb.opencga opencga-storage - 2.11.0-SNAPSHOT + 2.11.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 97db69b63b9..304c1557d11 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.11.0-SNAPSHOT + 2.11.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml index 1c27bd10350..26772d00f76 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.11.0-SNAPSHOT + 2.11.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml index f1f99b70468..c8f68af4a3b 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.11.0-SNAPSHOT + 2.11.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml index 03561e6c93d..f1ed98583f3 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.11.0-SNAPSHOT + 2.11.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml index c0e60a63db5..8553efb02eb 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml @@ -50,7 +50,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.11.0-SNAPSHOT + 2.11.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 1ea5e5a91d1..467b74c7698 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -28,7 +28,7 @@ org.opencb.opencga opencga-storage - 2.11.0-SNAPSHOT + 2.11.0 ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index c9a6b5604a3..4dffc327e82 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.11.0-SNAPSHOT + 2.11.0 ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index 49b680170d0..c7c836344e7 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.11.0-SNAPSHOT + 2.11.0 ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index caa613c03e2..98bf8c79755 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 2.11.0-SNAPSHOT + 2.11.0 ../pom.xml diff --git a/pom.xml b/pom.xml index c0b9f02fd71..6c799623f4d 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.11.0-SNAPSHOT + 2.11.0 pom OpenCGA OpenCGA projects implements a big data platform for genomic data analysis @@ -42,12 +42,12 @@ - 2.11.0_dev - 2.11.0_dev - 5.7.0-SNAPSHOT - 2.11.0-SNAPSHOT - 4.11.0-SNAPSHOT - 2.11.0-SNAPSHOT + 2.11.0 + 2.11.0 + 5.7.0 + 2.11.0 + 4.11.0 + 2.11.0 0.2.0 From bce2a4765bcfc2ef53c8f09730b4fff19d6a815c Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 20 Sep 2023 13:30:45 +0200 Subject: [PATCH 105/109] Prepare new development branch release-2.11.x --- opencga-analysis/pom.xml | 2 +- opencga-app/pom.xml | 2 +- opencga-catalog/pom.xml | 2 +- opencga-client/pom.xml | 2 +- opencga-clinical/pom.xml | 2 +- opencga-core/pom.xml | 2 +- opencga-master/pom.xml | 2 +- opencga-server/pom.xml | 2 +- opencga-storage/opencga-storage-app/pom.xml | 2 +- opencga-storage/opencga-storage-benchmark/pom.xml | 2 +- opencga-storage/opencga-storage-core/pom.xml | 2 +- .../opencga-storage-hadoop-core/pom.xml | 2 +- .../opencga-storage-hadoop-deps-emr6.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp2.6/pom.xml | 2 +- .../opencga-storage-hadoop-deps-hdp3.1/pom.xml | 2 +- .../opencga-storage-hadoop-deps/pom.xml | 2 +- opencga-storage/opencga-storage-hadoop/pom.xml | 2 +- opencga-storage/opencga-storage-server/pom.xml | 2 +- opencga-storage/pom.xml | 2 +- opencga-test/pom.xml | 2 +- pom.xml | 14 +++++++------- 21 files changed, 27 insertions(+), 27 deletions(-) diff --git a/opencga-analysis/pom.xml b/opencga-analysis/pom.xml index 75aeacc0f1b..69f3bd0df08 100644 --- a/opencga-analysis/pom.xml +++ b/opencga-analysis/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.11.0 + 2.12.0-SNAPSHOT ../pom.xml diff --git a/opencga-app/pom.xml b/opencga-app/pom.xml index 1c574488bb2..fe7211f3a68 100644 --- a/opencga-app/pom.xml +++ b/opencga-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.11.0 + 2.12.0-SNAPSHOT ../pom.xml diff --git a/opencga-catalog/pom.xml b/opencga-catalog/pom.xml index 6fdf8029ab9..f44b772294c 100644 --- a/opencga-catalog/pom.xml +++ b/opencga-catalog/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga - 2.11.0 + 2.12.0-SNAPSHOT ../pom.xml diff --git a/opencga-client/pom.xml b/opencga-client/pom.xml index b7e5033cc84..c3d5e42f079 100644 --- a/opencga-client/pom.xml +++ b/opencga-client/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.11.0 + 2.12.0-SNAPSHOT ../pom.xml diff --git a/opencga-clinical/pom.xml b/opencga-clinical/pom.xml index 1e1394cc92a..11653f27526 100644 --- a/opencga-clinical/pom.xml +++ b/opencga-clinical/pom.xml @@ -5,7 +5,7 @@ org.opencb.opencga opencga - 2.11.0 + 2.12.0-SNAPSHOT ../pom.xml 4.0.0 diff --git a/opencga-core/pom.xml b/opencga-core/pom.xml index 2d131098bbd..169c804bd9f 100644 --- a/opencga-core/pom.xml +++ b/opencga-core/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.11.0 + 2.12.0-SNAPSHOT ../pom.xml diff --git a/opencga-master/pom.xml b/opencga-master/pom.xml index 0ea519d70d4..d12a8eb58d6 100644 --- a/opencga-master/pom.xml +++ b/opencga-master/pom.xml @@ -22,7 +22,7 @@ opencga org.opencb.opencga - 2.11.0 + 2.12.0-SNAPSHOT ../pom.xml diff --git a/opencga-server/pom.xml b/opencga-server/pom.xml index 2d636201f53..4d4280c8895 100644 --- a/opencga-server/pom.xml +++ b/opencga-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.11.0 + 2.12.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-app/pom.xml b/opencga-storage/opencga-storage-app/pom.xml index 5a2f15e6fac..e0d6b60b973 100644 --- a/opencga-storage/opencga-storage-app/pom.xml +++ b/opencga-storage/opencga-storage-app/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.11.0 + 2.12.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-benchmark/pom.xml b/opencga-storage/opencga-storage-benchmark/pom.xml index 00921cbe8e6..d2b371a6c79 100644 --- a/opencga-storage/opencga-storage-benchmark/pom.xml +++ b/opencga-storage/opencga-storage-benchmark/pom.xml @@ -22,7 +22,7 @@ opencga-storage org.opencb.opencga - 2.11.0 + 2.12.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-core/pom.xml b/opencga-storage/opencga-storage-core/pom.xml index 0875ba3e255..3ba6bfd88e0 100644 --- a/opencga-storage/opencga-storage-core/pom.xml +++ b/opencga-storage/opencga-storage-core/pom.xml @@ -25,7 +25,7 @@ org.opencb.opencga opencga-storage - 2.11.0 + 2.12.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml index 304c1557d11..e04af6512de 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-core/pom.xml @@ -23,7 +23,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.11.0 + 2.12.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml index 26772d00f76..76ffc1e9ce3 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-emr6.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.11.0 + 2.12.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml index c8f68af4a3b..09519b23291 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp2.6/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.11.0 + 2.12.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml index f1ed98583f3..8d284fb1f33 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/opencga-storage-hadoop-deps-hdp3.1/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage-hadoop-deps - 2.11.0 + 2.12.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml index 8553efb02eb..132c0f14681 100644 --- a/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/opencga-storage-hadoop-deps/pom.xml @@ -50,7 +50,7 @@ org.opencb.opencga opencga-storage-hadoop - 2.11.0 + 2.12.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-hadoop/pom.xml b/opencga-storage/opencga-storage-hadoop/pom.xml index 467b74c7698..05620a5144b 100644 --- a/opencga-storage/opencga-storage-hadoop/pom.xml +++ b/opencga-storage/opencga-storage-hadoop/pom.xml @@ -28,7 +28,7 @@ org.opencb.opencga opencga-storage - 2.11.0 + 2.12.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/opencga-storage-server/pom.xml b/opencga-storage/opencga-storage-server/pom.xml index 4dffc327e82..0d55a15b610 100644 --- a/opencga-storage/opencga-storage-server/pom.xml +++ b/opencga-storage/opencga-storage-server/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga-storage - 2.11.0 + 2.12.0-SNAPSHOT ../pom.xml diff --git a/opencga-storage/pom.xml b/opencga-storage/pom.xml index c7c836344e7..697f00a8e51 100644 --- a/opencga-storage/pom.xml +++ b/opencga-storage/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.11.0 + 2.12.0-SNAPSHOT ../pom.xml diff --git a/opencga-test/pom.xml b/opencga-test/pom.xml index 98bf8c79755..a1797410a10 100644 --- a/opencga-test/pom.xml +++ b/opencga-test/pom.xml @@ -24,7 +24,7 @@ org.opencb.opencga opencga - 2.11.0 + 2.12.0-SNAPSHOT ../pom.xml diff --git a/pom.xml b/pom.xml index 6c799623f4d..890c5a2102b 100644 --- a/pom.xml +++ b/pom.xml @@ -22,7 +22,7 @@ org.opencb.opencga opencga - 2.11.0 + 2.12.0-SNAPSHOT pom OpenCGA OpenCGA projects implements a big data platform for genomic data analysis @@ -42,12 +42,12 @@ - 2.11.0 - 2.11.0 - 5.7.0 - 2.11.0 - 4.11.0 - 2.11.0 + 2.12.0_dev + 2.12.0_dev + 5.8.0-SNAPSHOT + 2.12.0-SNAPSHOT + 4.12.0-SNAPSHOT + 2.12.0-SNAPSHOT 0.2.0 From e830904e1df1dd31dca636705efab7913270586a Mon Sep 17 00:00:00 2001 From: Juanfe Sanahuja <85166064+juanfeSanahuja@users.noreply.github.com> Date: Wed, 20 Sep 2023 19:34:45 +0200 Subject: [PATCH 106/109] Update test-analysis.yml --- .github/workflows/test-analysis.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/test-analysis.yml b/.github/workflows/test-analysis.yml index a83cea15dc9..fe6350d59ca 100644 --- a/.github/workflows/test-analysis.yml +++ b/.github/workflows/test-analysis.yml @@ -75,6 +75,8 @@ jobs: run: mvn -B verify surefire-report:report --fail-never -P storage-hadoop,hdp3.1,${{ inputs.test_profile }} -Dcheckstyle.skip -Popencga-storage-hadoop-deps -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' ${{ inputs.mvn_opts }} - name: Publish Test Report uses: scacap/action-surefire-report@v1 + env: + NODE_OPTIONS: '--max_old_space_size=4096' ## Skip cancelled() ## https://docs.github.com/en/actions/learn-github-actions/expressions#cancelled if: success() || failure() From df56810cef4f15f77d38a8b30c2250b1275b3f51 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 4 Oct 2023 12:53:25 +0200 Subject: [PATCH 107/109] cicd: workflow_dispatch: #TASK-5092 --- .github/workflows/pull-request-merge.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/pull-request-merge.yml b/.github/workflows/pull-request-merge.yml index 3e3e5bb46b9..cf334ca8ed6 100644 --- a/.github/workflows/pull-request-merge.yml +++ b/.github/workflows/pull-request-merge.yml @@ -7,6 +7,7 @@ on: - release-* types: - closed + workflow_dispatch: jobs: build: From ba5d9ec65ff731da2996b3caf1a9bc5ee12d5cbd Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 4 Oct 2023 13:36:20 +0200 Subject: [PATCH 108/109] cicd: Pull Request Merge Workflow workflow_dispatch #TASK-5092 --- .github/workflows/pull-request-merge.yml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/.github/workflows/pull-request-merge.yml b/.github/workflows/pull-request-merge.yml index cf334ca8ed6..7d6fcb8818f 100644 --- a/.github/workflows/pull-request-merge.yml +++ b/.github/workflows/pull-request-merge.yml @@ -3,18 +3,21 @@ name: "Pull Request Merge Workflow" on: pull_request: branches: - - develop - - release-* + - "develop" + - "release-*" types: - closed workflow_dispatch: jobs: build: - uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop + uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.8.x + with: + maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' delete-docker: - uses: opencb/java-common-libs/.github/workflows/delete-docker-hub-workflow.yml@develop + uses: opencb/java-common-libs/.github/workflows/delete-docker-hub-workflow.yml@release-4.8.x + needs: build with: cli: python3 ./build/cloud/docker/docker-build.py delete --images base --tag ${{ github.head_ref }} secrets: inherit From ce32db4042b07fd7fa60fc1927a67070f63ac871 Mon Sep 17 00:00:00 2001 From: JuanfeSanahuja Date: Wed, 4 Oct 2023 17:46:09 +0200 Subject: [PATCH 109/109] cicd: undo step by step #TASK-5092 --- .github/workflows/pull-request-merge.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pull-request-merge.yml b/.github/workflows/pull-request-merge.yml index 7d6fcb8818f..c3ca5077a33 100644 --- a/.github/workflows/pull-request-merge.yml +++ b/.github/workflows/pull-request-merge.yml @@ -11,12 +11,12 @@ on: jobs: build: - uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.8.x + uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop with: maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6' delete-docker: - uses: opencb/java-common-libs/.github/workflows/delete-docker-hub-workflow.yml@release-4.8.x + uses: opencb/java-common-libs/.github/workflows/delete-docker-hub-workflow.yml@develop needs: build with: cli: python3 ./build/cloud/docker/docker-build.py delete --images base --tag ${{ github.head_ref }}